Rename & re-engineer misleading "beacon" Translator format

The _Translator class defines a beacon string format which has no known relationship to the Beacon standard but apparently mimics a non-codified use in the query fields of some front-end implementations (but does not conform to any Beacon definition):

r"(?P<chr>[^-]+)\s*:\s*(?P<pos>\d+)\s*(?P<ref>\w+)\s*>\s*(?P<alt>\w+)"

The Beacon specification allows the definition of genomic variations as

      - $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'

... where a LegacyVariation is an object with properties location (i.e. .../vrs/1.3/vrs.json#/definitions/Location), variantType, referenceBases and alternateBases.

Recommendation

rename the misleading beacon translator to beacon-legacy
define an appropriate input format, preferably as an object using the Beacon v2 definition (or a stringified/list version of this) and integrate it with the appropriate method
coordinate with/ the Beacon developers :-)

Bump. Maybe best: Just delete the whole beacon format; as one of the leads of the Beacon spec. I feel this should be done speedily since it totally distorts the referenced concept.

And then work w/ us to look into a versioned Beacon object format or develop sensible stringified standards.

I'd be fine removing. It looks like it was added 6 years ago in 8865107 . I'm not sure if anyone really uses the beacon format for translation (I really only know of hgvs/spdi/gnomad being used frequently)

@mbaudis

I agree. Please remove. @mbaudis we will rely on you and the beacon crew to let us know if/when you would like to reintroduce a 'beacon' nomenclature

feat!: remove support for beacon translation

See #578

@korikuzma

@korikuzma @larrybabb Thanks! Closing ...

feat: add deprecation warning for beacon translation (#578)

Navigation Menu

Repository navigation

Rename & re-engineer misleading "beacon" Translator format #568

Recommendation

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Rename & re-engineer misleading "beacon" Translator format #568

Description

Recommendation

Activity

mbaudis commented on Aug 14, 2025

korikuzma commented on Aug 14, 2025

larrybabb commented on Aug 15, 2025

korikuzma commented on Aug 15, 2025

mbaudis commented on Aug 18, 2025

Metadata

Metadata

Assignees

Labels

Type

Projects

Milestone

Relationships

Development

Issue actions