diff --git a/schemas/BeaconAlleleRequest.yaml b/schemas/LegacyAlleleRequest.yaml similarity index 100% rename from schemas/BeaconAlleleRequest.yaml rename to schemas/LegacyAlleleRequest.yaml diff --git a/schemas/VariantBracketRequest.yaml b/schemas/LegacyBracketRequest.yaml similarity index 100% rename from schemas/VariantBracketRequest.yaml rename to schemas/LegacyBracketRequest.yaml diff --git a/schemas/LegacyRangeRequest.yaml b/schemas/LegacyRangeRequest.yaml new file mode 100644 index 0000000..bb3d537 --- /dev/null +++ b/schemas/LegacyRangeRequest.yaml @@ -0,0 +1,41 @@ +$schema: https://json-schema.org/draft/2020-12/schema +$id: https://genomebeacons.org/schemas/beacon/BeaconRangeRequest/v1.1.0 +title: VariantRangeRequest +description: >- + A request for matching variants in a genomic range. This request type requires + to provide *exactly* 1 `start` and 1 `end` position, which are both 0-based and + define the base range with which variants should be associated. The exact way + of variant association (e.g. complete or partial overlap or even proximity) is + being left to the individual implementations and use cases. + Beacon version: v2.0 + Future considerations: There are some inherited ambiguities + * `assemblyId` and `referenceName` should be deprectated in favour of a versioned + `sequenceId` + * the shared use of the `start` and `end` parameters for both base positions and + bracket positions is not ideal - here addressed by the `sequencePosition` type + but still existing in parameters +type: object +required: + - referenceName + - start + - end + +properties: + referenceName: + $ref: variantRequestParameters.yaml#/$defs/referenceName + start: + $ref: variantRequestParameters.yaml#/$defs/sequencePosition + end: + $ref: variantRequestParameters.yaml#/$defs/sequencePosition + alternateBases: + $ref: variantRequestParameters.yaml#/$defs/alternateBases + variantType: + $ref: variantRequestParameters.yaml#/$defs/variantType + assemblyId: + $ref: variantRequestParameters.yaml#/$defs/assemblyId + +examples: + - referenceName: 17 + assemblyId: GRCh38 + start: [7572826] + end: [7579005] diff --git a/schemas/VariantRangeRequest.yaml b/schemas/VariantRangeRequest.yaml index bb3d537..8726367 100644 --- a/schemas/VariantRangeRequest.yaml +++ b/schemas/VariantRangeRequest.yaml @@ -7,32 +7,27 @@ description: >- define the base range with which variants should be associated. The exact way of variant association (e.g. complete or partial overlap or even proximity) is being left to the individual implementations and use cases. - Beacon version: v2.0 - Future considerations: There are some inherited ambiguities - * `assemblyId` and `referenceName` should be deprectated in favour of a versioned + Beacon version: v2.n + There are some inherited ambiguities + * referenceName` should be deprectated in favour of a versioned `sequenceId` * the shared use of the `start` and `end` parameters for both base positions and bracket positions is not ideal - here addressed by the `sequencePosition` type but still existing in parameters type: object required: - - referenceName - - start - - end + - sequenceId + - sequenceInterval properties: - referenceName: + sequenceId: $ref: variantRequestParameters.yaml#/$defs/referenceName - start: - $ref: variantRequestParameters.yaml#/$defs/sequencePosition - end: - $ref: variantRequestParameters.yaml#/$defs/sequencePosition - alternateBases: + sequenceInterval: + $ref: variantRequestParameters.yaml#/$defs/sequenceInterval + sequence: $ref: variantRequestParameters.yaml#/$defs/alternateBases variantType: $ref: variantRequestParameters.yaml#/$defs/variantType - assemblyId: - $ref: variantRequestParameters.yaml#/$defs/assemblyId examples: - referenceName: 17 diff --git a/schemas/variantRequestParameters.yaml b/schemas/variantRequestParameters.yaml index 9861c78..f417ad6 100644 --- a/schemas/variantRequestParameters.yaml +++ b/schemas/variantRequestParameters.yaml @@ -93,7 +93,7 @@ $defs: minItems: 1 maxItems: 1 - sequenceBracket: + sequenceInterval: description: This is an explicit 2-values version of the `basePositions` generic, for use in e.g. `VariantBracketRequest`.