From 407263b94f1c5f2d1e0b024a17df3e8dc78dfa3f Mon Sep 17 00:00:00 2001 From: Elissa Alarmani Date: Sun, 29 Oct 2023 13:32:22 -0400 Subject: [PATCH] finalize testing files --- .../CopyNumberVariantPage.spec.tsx.snap | 186 +- browser/src/GenePage/GenePage.spec.tsx | 66 +- .../__snapshots__/GenePage.spec.tsx.snap | 2501 ++++-- ...riantCooccurrenceCountsTable.spec.tsx.snap | 8 + .../MitochondrialVariantPage.spec.tsx.snap | 884 ++- .../__snapshots__/RegionPage.spec.tsx.snap | 2 + browser/src/Searchbox.spec.tsx | 2 +- .../StructuralVariantPage.spec.tsx.snap | 408 + .../TranscriptPage.spec.tsx.snap | 1296 ++-- .../TranscriptPageContainer.spec.tsx.snap | 950 ++- browser/src/__factories__/Gene.ts | 2 + .../DatasetSelector.spec.tsx.snap | 6774 +++-------------- .../src/__snapshots__/HomePage.spec.tsx.snap | 5 + .../src/__snapshots__/NavBar.spec.tsx.snap | 5 + .../src/__snapshots__/Searchbox.spec.tsx.snap | 251 + browser/src/variantFeedback.spec.ts | 4 +- dataset-metadata/metadata.spec.ts | 2 +- dataset-metadata/metadata.ts | 3 + 18 files changed, 5870 insertions(+), 7479 deletions(-) diff --git a/browser/src/CopyNumberVariantPage/__snapshots__/CopyNumberVariantPage.spec.tsx.snap b/browser/src/CopyNumberVariantPage/__snapshots__/CopyNumberVariantPage.spec.tsx.snap index e0bdfbf30..4f47b0274 100644 --- a/browser/src/CopyNumberVariantPage/__snapshots__/CopyNumberVariantPage.spec.tsx.snap +++ b/browser/src/CopyNumberVariantPage/__snapshots__/CopyNumberVariantPage.spec.tsx.snap @@ -33,7 +33,7 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -237,14 +254,6 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D 0.3565 -
    -
    - Quality score -
    -
    - 99 -
    -
    Position @@ -422,6 +431,24 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D +
    +
    +

    + Consequences +

    +

    + This variant has consequences in + 0 + gene + s + . +

    +
    +
    `; @@ -458,7 +485,7 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -662,14 +706,6 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D 0.3565 -
    -
    - Quality score -
    -
    - 99 -
    -
    Position @@ -847,5 +883,23 @@ exports[`CopyNumberVariantPage with dataset gnomad_cnv_r4 with variant of type D +
    +
    +

    + Consequences +

    +

    + This variant has consequences in + 0 + gene + s + . +

    +
    +
    `; diff --git a/browser/src/GenePage/GenePage.spec.tsx b/browser/src/GenePage/GenePage.spec.tsx index 1f6f83cba..f4ace7de3 100644 --- a/browser/src/GenePage/GenePage.spec.tsx +++ b/browser/src/GenePage/GenePage.spec.tsx @@ -71,6 +71,9 @@ forDatasetsNotMatching(svRegexp, 'GenePage with non-SV dataset "%s"', (datasetId coverage: {}, }, }), + CopyNumberVariantsInGene: () => ({ + gene: { copy_number_variants: [] }, + }), }) ) @@ -126,47 +129,52 @@ forDatasetsMatching(svRegexp, 'GenePage with SV dataset "%s"', (datasetId) => { }) }) - forDatasetsMatching(cnvRegexp, 'GenePage with CNV dataset "%s"', (datasetId) => { - test('has no unexpected changes', () => { - const gene = geneFactory.build() - setMockApiResponses({ - CopyNumberVariantsInGene: () => ({ - gene: { copy_number_variants: [] }, - }), - RegionCoverage: () => ({ - region: { - coverage: {}, - }, - }), - }) - const tree = renderer.create( - withDummyRouter() - ) - expect(tree).toMatchSnapshot() - }) - - test('queries the API for region coverage with the correct parameters', async () => { +forDatasetsMatching(cnvRegexp, 'GenePage with CNV dataset "%s"', (datasetId) => { + test('has no unexpected changes', () => { const gene = geneFactory.build() setMockApiResponses({ - StructuralVariantsInGene: () => ({ - gene: { structural_variants: [] }, + CopyNumberVariantsInGene: () => ({ + gene: { copy_number_variants: [] }, }), RegionCoverage: () => ({ region: { coverage: {}, }, }), + GeneCoverage: () => ({ + gene: { + coverage: {}, + }, + }), + }) + const tree = renderer.create( + withDummyRouter() + ) + expect(tree).toMatchSnapshot() + }) + + test('queries the API for region coverage with the correct parameters', async () => { + const gene = geneFactory.build() + setMockApiResponses({ + CopyNumberVariantsInGene: () => ({ + gene: { copy_number_variants: [] }, + }), + GeneCoverage: () => ({ + gene: { + coverage: {}, + }, + }), }) renderer.create( withDummyRouter() ) const coverageQueries = mockApiCalls().filter( - ({ operationName }) => operationName === 'RegionCoverage' + ({ operationName }) => operationName === 'GeneCoverage' ) expect(coverageQueries).toHaveLength(1) const [coverageQuery] = coverageQueries const exomeCoverageArg = coverageQuery.variables.includeExomeCoverage - expect(exomeCoverageArg).toEqual(false) + expect(exomeCoverageArg).toEqual(true) }) }) @@ -183,7 +191,7 @@ describe.each([ ['gnomad_r3_non_neuro', false], ['gnomad_r3_non_topmed', false], ['gnomad_r3_non_v2', false], - ['gnomad_cnv_r4', false], + ['gnomad_cnv_r4', true], ] as [DatasetId, boolean][])('GenePage with non-SV dataset "%s"', (datasetId, expectedResult) => { test('queries the API for gene coverage with the correct parameters', async () => { const gene = geneFactory.build() @@ -197,6 +205,9 @@ describe.each([ coverage: {}, }, }), + CopyNumberVariantsInGene: () => ({ + gene: { copy_number_variants: [] }, + }), }) renderer.create( withDummyRouter() @@ -228,7 +239,7 @@ describe.each([ ['gnomad_r3_non_neuro', 'GRCh38', true], ['gnomad_r3_non_topmed', 'GRCh38', true], ['gnomad_r3_non_v2', 'GRCh38', true], - ['gnomad_cnv_r4','GRCh38', false], + ['gnomad_cnv_r4', 'GRCh38', false], ] as [DatasetId, ReferenceGenome, boolean][])( 'gene query with dataset %s', (datasetId, expectedReferenceGenome, expectedIncludeShortTandemRepeats) => { @@ -254,4 +265,5 @@ describe.each([ expectedIncludeShortTandemRepeats ) }) - }) + } +) diff --git a/browser/src/GenePage/__snapshots__/GenePage.spec.tsx.snap b/browser/src/GenePage/__snapshots__/GenePage.spec.tsx.snap index df36e4d8b..b6d6eb7e2 100644 --- a/browser/src/GenePage/__snapshots__/GenePage.spec.tsx.snap +++ b/browser/src/GenePage/__snapshots__/GenePage.spec.tsx.snap @@ -1,6 +1,6 @@ // Jest Snapshot v1, https://goo.gl/fbAQLP -exports[`GenePage with SV dataset "gnomad_sv_r2_1" has no unexpected changes 1`] = ` +exports[`GenePage with CNV dataset "gnomad_cnv_r4" has no unexpected changes 1`] = `
    @@ -40,12 +40,12 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1" has no unexpected changes 1`] - gnomAD v2.1.1 + gnomAD v3.1.2
  • - gnomAD SVs v2.1 + gnomAD exome CNVs v4.0
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -699,6 +692,17 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1" has no unexpected changes 1`]
    + Viewing full + gene + . + +
    @@ -860,7 +864,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1" has no unexpected changes 1`] } > @@ -1286,8 +1290,8 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1" has no unexpected changes 1`] stroke="#333" x1={0} x2={799} - y1={200} - y2={200} + y1={190} + y2={190} /> @@ -1449,7 +1453,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1" has no unexpected changes 1`]
    `; -exports[`GenePage with SV dataset "gnomad_sv_r2_1_controls" has no unexpected changes 1`] = ` +exports[`GenePage with SV dataset "gnomad_sv_r2_1" has no unexpected changes 1`] = `
    @@ -1750,13 +1754,13 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1_controls" has no unexpected ch > - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -2898,7 +2895,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1_controls" has no unexpected ch
    `; -exports[`GenePage with SV dataset "gnomad_sv_r2_1_non_neuro" has no unexpected changes 1`] = ` +exports[`GenePage with SV dataset "gnomad_sv_r2_1_controls" has no unexpected changes 1`] = `
    @@ -3199,13 +3196,13 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1_non_neuro" has no unexpected c > - gnomAD SVs v2.1 (non-neuro) + gnomAD SVs v2.1 (controls)
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -3635,7 +3625,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r2_1_non_neuro" has no unexpected c className="Select-sc-1lkyg9e-0 ivadCR" id="coverage-metric" onChange={[Function]} - value="mean" + value="over_30" > `; -exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = ` +exports[`GenePage with SV dataset "gnomad_sv_r2_1_non_neuro" has no unexpected changes 1`] = `
    @@ -4387,12 +4377,12 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = - gnomAD v3.1.2 + gnomAD v2.1.1
  • - gnomAD SVs v4 + gnomAD SVs v2.1 (non-neuro)
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • - Constraint not yet available for gnomAD v3. + Constraint not available for this + gene

  • @@ -5059,7 +5067,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = className="Select-sc-1lkyg9e-0 ivadCR" id="coverage-metric" onChange={[Function]} - value="mean" + value="over_30" > - Per-base mean depth of coverage + Fraction of individuals with coverage over 30
    - 10 + 0.1 @@ -5264,7 +5272,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 20 + 0.2 @@ -5304,7 +5312,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 30 + 0.3 @@ -5344,7 +5352,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 40 + 0.4 @@ -5384,7 +5392,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 50 + 0.5 @@ -5424,7 +5432,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 60 + 0.6 @@ -5464,7 +5472,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 70 + 0.7 @@ -5504,7 +5512,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 80 + 0.8 @@ -5544,7 +5552,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 90 + 0.9 @@ -5584,7 +5592,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 100 + 1.0 @@ -6132,6 +6140,23 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] =
    +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • - Per-base mean depth of coverage + Fraction of individuals with coverage over 30
    - 10 + 0.1 @@ -6688,7 +6713,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 20 + 0.2 @@ -6728,7 +6753,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 30 + 0.3 @@ -6768,7 +6793,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 40 + 0.4 @@ -6808,7 +6833,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 50 + 0.5 @@ -6848,7 +6873,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 60 + 0.6 @@ -6888,7 +6913,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 70 + 0.7 @@ -6928,7 +6953,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 80 + 0.8 @@ -6968,7 +6993,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 90 + 0.9 @@ -7008,7 +7033,7 @@ exports[`GenePage with SV dataset "gnomad_sv_r4" has no unexpected changes 1`] = dy="0em" x={-8} > - 100 + 1.0 @@ -7496,7 +7521,7 @@ exports[`GenePage with non-SV dataset "exac" has no unexpected changes 1`] = ` >
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -8678,7 +8696,7 @@ exports[`GenePage with non-SV dataset "exac" has no unexpected changes 1`] = ` `; -exports[`GenePage with non-SV dataset "gnomad_r2_1" has no unexpected changes 1`] = ` +exports[`GenePage with non-SV dataset "gnomad_cnv_r4" has no unexpected changes 1`] = `
    @@ -8713,21 +8731,21 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1" has no unexpected changes 1` className="DatasetSelector__NavigationMenuWrapper-sc-1p2fxbn-0 ebZvwy" >
  • - gnomAD v2.1.1 + gnomAD v3.1.2
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -10129,65 +10140,1518 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1" has no unexpected changes 1`
    -
    +
    +
    + +`; + +exports[`GenePage with non-SV dataset "gnomad_r2_1" has no unexpected changes 1`] = ` +
    +
    +
    +
    +

    -
    +

    +
    +
    + + Dataset + +
    -
    -
    -
    + + + +
  • + + gnomAD exome CNVs v4.0 + +
  • +
  • + + + + + + +
  • + + + + +
    +
    +
    +
    +
    +
    +
    + Genome build +
    +
    + GRCh37 + / + hg19 +
    +
    +
    +
    + Ensembl gene ID +
    +
    + dummy_gene-1 + . + 5.6.7.8 +
    +
    +
    +
    + Symbol in GENCODE v19 +
    +
    +
    +
    +
    + Ensembl canonical transcript + +
    +
    + + transcript-999 + . + 12.34.5 + +
    +
    +
    +
    + Region +
    +
    + + 13 + : + 123 + - + 321 + +
    +
    +
    +
    + External resources +
    +
    + + Ensembl + + , + + + UCSC Browser + + , + + +
    +
    +
    +
    +
    +
    +
    + Constraint + +
    +
    + Variant co-occurrence + +
    +
    +

    + Constraint not available for this + gene +

    +
    +
    +
    + Viewing full + gene + . + + +
    +
    +
    +
    +
    +
      + + +
    +
    +
    +
    +
    + Fraction of individuals with coverage over 30 +
    +
    +
    +
    + + + + + + + + 0.1 + + + + + + + + + + 0.2 + + + + + + + + + + 0.3 + + + + + + + + + + 0.4 + + + + + + + + + + 0.5 + + + + + + + + + + 0.6 + + + + + + + + + + 0.7 + + + + + + + + + + 0.8 + + + + + + + + + + 0.9 + + + + + + + + + + 1.0 + + + + + + + + + + + +
    +
    +
    +
    +
    + Include: +
      +
    • + +
    • +
    • + +
    • +
    • + +
    • +
    +
    +
    +
    +
    +
    +
    + + Positive strand +
    +
    +
    +
    + + + +
    +
    +
    +
    +
    +
    +
    +
    +
    + + Regional missense constraint + + +
    +
    +
    +
    + gnomAD SVs v4 +
    + 63,046 samples +
    + + +
  • + - gnomAD SVs v4 + gnomAD exome CNVs v4.0
    - 63,046 samples + 464,566 samples
  • @@ -10676,30 +12157,6 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1_controls" has no unexpected c -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -12135,7 +13592,7 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1_non_cancer" has no unexpected > +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -13713,7 +15163,7 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1_non_neuro" has no unexpected > +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -15291,7 +16734,7 @@ exports[`GenePage with non-SV dataset "gnomad_r2_1_non_topmed" has no unexpected > +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -16870,12 +18306,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3" has no unexpected changes 1`] - gnomAD SVs v4 + gnomAD exome CNVs v4.0
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -18352,12 +19781,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_controls_and_biobanks" has no u - gnomAD SVs v4 + gnomAD exome CNVs v4.0
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • 8,342 samples
    - -
  • -
  • - - gnomAD SVs v2.1 (controls) -
    - 5,192 samples -
    -
    -
  • - -
  • -
    - GRCh38 -
    + +
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (controls)
    - 464,566 samples + 5,192 samples
  • @@ -19834,12 +21256,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_non_cancer" has no unexpected c - gnomAD SVs v4 + gnomAD exome CNVs v4.0
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -21316,12 +22731,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_non_neuro" has no unexpected ch - gnomAD SVs v4 + gnomAD exome CNVs v4.0
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -22798,12 +24206,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_non_topmed" has no unexpected c - gnomAD SVs v4 + gnomAD exome CNVs v4.0
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -24280,12 +25681,12 @@ exports[`GenePage with non-SV dataset "gnomad_r3_non_v2" has no unexpected chang - gnomAD SVs v4 + gnomAD exome CNVs v4.0
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -25761,7 +27155,7 @@ exports[`GenePage with non-SV dataset "gnomad_r4" has no unexpected changes 1`] > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • diff --git a/browser/src/GenePage/__snapshots__/VariantCooccurrenceCountsTable.spec.tsx.snap b/browser/src/GenePage/__snapshots__/VariantCooccurrenceCountsTable.spec.tsx.snap index 183801efc..adb4b2029 100644 --- a/browser/src/GenePage/__snapshots__/VariantCooccurrenceCountsTable.spec.tsx.snap +++ b/browser/src/GenePage/__snapshots__/VariantCooccurrenceCountsTable.spec.tsx.snap @@ -2050,6 +2050,14 @@ exports[`VariantCoocurrenceCountsTable with non v2 dataset "gnomad_r3_non_v2" ha `; +exports[`VariantCoocurrenceCountsTable with non v2 dataset "gnomad_r4" has no unexpected changes and renders as placeholder text 1`] = ` + +

    + Variant co-occurrence is only available for gnomAD v2. +

    +
    +`; + exports[`VariantCoocurrenceCountsTable with non v2 dataset "gnomad_sv_r4" has no unexpected changes and renders as placeholder text 1`] = `

    diff --git a/browser/src/MitochondrialVariantPage/__snapshots__/MitochondrialVariantPage.spec.tsx.snap b/browser/src/MitochondrialVariantPage/__snapshots__/MitochondrialVariantPage.spec.tsx.snap index d7b6836ac..f5995e291 100644 --- a/browser/src/MitochondrialVariantPage/__snapshots__/MitochondrialVariantPage.spec.tsx.snap +++ b/browser/src/MitochondrialVariantPage/__snapshots__/MitochondrialVariantPage.spec.tsx.snap @@ -125,7 +125,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_cnv_r4 has no unexpected c > - GRCh37 + GRCh38

  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -8402,7 +8419,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3 has no unexpected chang > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -16589,7 +16623,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_controls_and_biobanks h > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -24776,7 +24827,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_non_cancer has no unexp > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -32963,7 +33031,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_non_neuro has no unexpe > +
  • +
    + GRCh38 +
    +
  • + + gnomAD SVs v4 +
    + 63,046 samples +
    +
    +
  • +
  • + + gnomAD exome CNVs v4.0 +
    + 464,566 samples +
    +
    +
  • +
  • -
  • -
    - GRCh38 -
    -
  • - - gnomAD exome CNVs v4.0 -
    - 464,566 samples -
    -
    -
  • - @@ -41150,7 +41235,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_non_topmed has no unexp > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -49337,7 +49439,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_r3_non_v2 has no unexpecte > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -57524,7 +57643,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_r4 has no unexpected chang > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -65711,7 +65847,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_sv_r2_1 has no unexpected > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -73898,7 +74051,7 @@ exports[`MitochondrialVariantPage with dataset gnomad_sv_r2_1_controls has no un > - GRCh37 + GRCh38
  • - gnomAD SVs v2.1 + gnomAD SVs v4
    - 10,847 samples + 63,046 samples
  • - gnomAD SVs v2.1 (non-neuro) + gnomAD exome CNVs v4.0
    - 8,342 samples + 464,566 samples
  • + +
  • +
    + GRCh37 +
  • - gnomAD SVs v2.1 (controls) + gnomAD SVs v2.1
    - 5,192 samples + 10,847 samples
  • - -
  • -
    - GRCh38 -
  • - gnomAD exome CNVs v4.0 + gnomAD SVs v2.1 (non-neuro)
    - 464,566 samples + 8,342 samples +
    +
    +
  • +
  • + + gnomAD SVs v2.1 (controls) +
    + 5,192 samples
  • @@ -82080,6 +82250,149 @@ exports[`MitochondrialVariantPage with dataset gnomad_sv_r2_1_non_neuro has no u +
  • + + gnomAD SVs v2.1 (non-neuro) + +
  • +
  • + + + + + + +