From c1a11c27c2dc9822e9406bfaf006790e8f998b3c Mon Sep 17 00:00:00 2001
From: Phil Darnowsky
Date: Thu, 26 Oct 2023 17:31:47 -0400
Subject: [PATCH] Change user-facing references to dataset to say "v4 SVs"
This includes the dataset ID `gnomad_sv_v4` itself as that appears in URLs.
---
.../structural-variants/sv-effect-overview.md | 8 +-
.../ConstraintTable.spec.tsx.snap | 12 +-
browser/src/DatasetSelector.tsx | 10 +-
.../__snapshots__/GenePage.spec.tsx.snap | 126 ++++-----
...riantCooccurrenceCountsTable.spec.tsx.snap | 2 +-
.../MitochondrialVariantPage.spec.tsx.snap | 2 +-
.../__snapshots__/ReadData.spec.tsx.snap | 8 +-
...chondrialRegionCoverageTrack.spec.tsx.snap | 4 +-
...itochondrialVariantsInRegion.spec.tsx.snap | 2 +-
.../__snapshots__/RegionPage.spec.tsx.snap | 20 +-
.../RegionPageContainer.spec.tsx.snap | 2 +-
browser/src/Searchbox.spec.tsx | 2 +-
browser/src/Searchbox.tsx | 6 +-
.../StructuralVariantPage.spec.tsx.snap | 144 +++++-----
...drialTranscriptCoverageTrack.spec.tsx.snap | 4 +-
...hondrialVariantsInTranscript.spec.tsx.snap | 2 +-
.../TranscriptPage.spec.tsx.snap | 2 +-
.../TranscriptPageContainer.spec.tsx.snap | 2 +-
.../DatasetSelector.spec.tsx.snap | 252 +++++++++---------
.../src/__snapshots__/HomePage.spec.tsx.snap | 4 +-
.../src/__snapshots__/NavBar.spec.tsx.snap | 4 +-
.../src/__snapshots__/Searchbox.spec.tsx.snap | 72 ++---
browser/src/identifiers.spec.ts | 4 +-
browser/src/identifiers.ts | 6 +-
browser/src/variantFeedback.spec.ts | 2 +-
dataset-metadata/metadata.spec.ts | 2 +-
dataset-metadata/metadata.ts | 36 +--
dataset-metadata/sampleCounts.ts | 2 +-
.../src/graphql/types/dataset-id.graphql | 2 +-
.../structural-variant-queries.spec.ts | 8 +-
.../src/queries/structural-variant-queries.ts | 4 +-
31 files changed, 378 insertions(+), 378 deletions(-)
diff --git a/browser/help/topics/structural-variants/sv-effect-overview.md b/browser/help/topics/structural-variants/sv-effect-overview.md
index c4df5b4b4..1eadc85c3 100644
--- a/browser/help/topics/structural-variants/sv-effect-overview.md
+++ b/browser/help/topics/structural-variants/sv-effect-overview.md
@@ -14,17 +14,17 @@ The functional consequence per SV was determined in the order below:
### Main functional consequences
1. ![](https://placehold.it/15/D43925/000000?text=+) **Predicted loss-of-function (pLoF)**: SV is predicted to delete the gene or truncate the gene product.
-2. ![](https://placehold.it/15/7459B2/000000?text=+) **Intragenic exonic duplication (IED)**: SV is predicted to result in duplicated exons within the gene, without extending beyond the boundaries of the open reading frame. (New in gnomAD v3)
-3. **Partial exon duplication (PED)**: SV is predicted to duplicate part of one or more exons without resulting in a whole-gene copy gain. (New in gnomAD v3)
+2. ![](https://placehold.it/15/7459B2/000000?text=+) **Intragenic exonic duplication (IED)**: SV is predicted to result in duplicated exons within the gene, without extending beyond the boundaries of the open reading frame. (New in gnomAD v4)
+3. **Partial exon duplication (PED)**: SV is predicted to duplicate part of one or more exons without resulting in a whole-gene copy gain. (New in gnomAD v4)
4. ![](https://placehold.it/15/2376B2/000000?text=+) **Copy gain (CG)**: SV is predicted to result in an entire additional intact copy of the gene.
### Other consequences
-4. **Transcription start site duplication**: SV is predicted to result in a duplication of a transcription start site but not result in any other, more severe consequences. (New in gnomAD v3).
+4. **Transcription start site duplication**: SV is predicted to result in a duplication of a transcription start site but not result in any other, more severe consequences. (New in gnomAD v4).
5. **MCNV overlap**: MCNV overlaps one or more protein-coding exons; exact consequence depends on the number of copies and their orientation.
6. **Partial duplication**: SV is predicted to partially duplicate the gene while leaving the original copy of the gene intact.
-7. **Exonic breakend**: breakend localizes to exonic locus, but consequence is unclear as SV is incompletely resolved. (New in gnomAD v3).
+7. **Exonic breakend**: breakend localizes to exonic locus, but consequence is unclear as SV is incompletely resolved. (New in gnomAD v4).
8. **UTR**: SV does not directly disrupt coding sequence, but overlaps one of the gene's untranslated regions (UTRs).
9. **Promoter**: SV does not directly disrupt coding sequence or promoter, but is within 2kb of the gene's transcription start site.
10. **Inversion span**: gene is entirely spanned by an inversion SV without being directly disrupted.
diff --git a/browser/src/ConstraintTable/__snapshots__/ConstraintTable.spec.tsx.snap b/browser/src/ConstraintTable/__snapshots__/ConstraintTable.spec.tsx.snap
index 06240663f..2505d48e5 100644
--- a/browser/src/ConstraintTable/__snapshots__/ConstraintTable.spec.tsx.snap
+++ b/browser/src/ConstraintTable/__snapshots__/ConstraintTable.spec.tsx.snap
@@ -6510,37 +6510,37 @@ exports[`ConstraintTable with "gnomad_sv_r2_1_non_neuro" dataset selected with a
`;
-exports[`ConstraintTable with "gnomad_sv_r3" dataset selected and gene with available constraint has no unexpected changes 1`] = `
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected and gene with available constraint has no unexpected changes 1`] = `
Constraint not yet available for gnomAD v3.
`;
-exports[`ConstraintTable with "gnomad_sv_r3" dataset selected and transcript with available constraint has no unexpected changes 1`] = `
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected and transcript with available constraint has no unexpected changes 1`] = `
Constraint not yet available for gnomAD v3.
`;
-exports[`ConstraintTable with "gnomad_sv_r3" dataset selected with a minimal gene has no unexpected changes 1`] = `
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a minimal gene has no unexpected changes 1`] = `
Constraint not yet available for gnomAD v3.
`;
-exports[`ConstraintTable with "gnomad_sv_r3" dataset selected with a minimal transcript has no unexpected changes 1`] = `
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a minimal transcript has no unexpected changes 1`] = `
Constraint not yet available for gnomAD v3.
`;
-exports[`ConstraintTable with "gnomad_sv_r3" dataset selected with a mitochondrial gene has no unexpected changes 1`] = `
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a mitochondrial gene has no unexpected changes 1`] = `
Constraint not yet available for gnomAD v3.
`;
-exports[`ConstraintTable with "gnomad_sv_r3" dataset selected with a mitochondrial transcript has no unexpected changes 1`] = `
+exports[`ConstraintTable with "gnomad_sv_r4" dataset selected with a mitochondrial transcript has no unexpected changes 1`] = `