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VRS references from 1.2 => 1.3 #186

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VRS references from 1.2 => 1.3 #186

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c634b81
VRS references from 1.2 => 1.3
mbaudis Nov 16, 2024
b1f81dc
removing the schema deparser changes
mbaudis Nov 16, 2024
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8 changes: 4 additions & 4 deletions models/json/beacon-v2-default-model/genomicVariations/defaultSchema.json
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Original file line number Diff line number Diff line change
@@ -1,5 +1,5 @@
{
"$comment": "version: ga4gh-beacon-variant-v2.0.0",
"$comment": "version: ga4gh-beacon-variant-v2.1.0",
"$defs": {
"CaseLevelVariant": {
"description": "",
Expand Down Expand Up @@ -272,7 +272,7 @@
"type": "string"
},
"location": {
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location"
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location"
},
"referenceBases": {
"description": "Reference bases for this variant (starting from `start`). * Accepted values: IUPAC codes for nucleotides (e.g. `https://www.bioinformatics.org/sms/iupac.html`). * N is a wildcard, that denotes the position of any base, and can be used\n as a standalone base of any type or within a partially known sequence.\n* an *empty value* is used in the case of insertions with the maximally\n trimmed, inserted sequence being indicated in `AlternateBases`.",
Expand Down Expand Up @@ -557,10 +557,10 @@
"variation": {
"oneOf": [
{
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation"
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation"
},
{
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation"
"$ref": "https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation"
},
{
"$ref": "#/$defs/LegacyVariation"
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8 changes: 4 additions & 4 deletions models/src/beacon-v2-default-model/genomicVariations/defaultSchema.yaml
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Original file line number Diff line number Diff line change
@@ -1,6 +1,6 @@
$schema: https://json-schema.org/draft/2020-12/schema
title: Genomic Variation
$comment: 'version: ga4gh-beacon-variant-v2.0.0'
$comment: 'version: ga4gh-beacon-variant-v2.1.0'
description: >-
Schema for a genomic variant entry.
type: object
Expand All @@ -10,8 +10,8 @@ required:
properties:
variation:
oneOf:
- $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/MolecularVariation
- $ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/SystemicVariation
- $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/MolecularVariation
- $ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/SystemicVariation
- $ref: '#/$defs/LegacyVariation'
variantInternalId:
description: >-
Expand Down Expand Up @@ -51,7 +51,7 @@ $defs:
- location
properties:
location:
$ref: https://w3id.org/ga4gh/schema/vrs/1.2/vrs.json#/definitions/Location
$ref: https://w3id.org/ga4gh/schema/vrs/1.3/vrs.json#/definitions/Location
variantType:
description: >-
The `variantType` declares the nature of the variation in relation
Expand Down
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