VRS references from 1.2 => 1.3 #186
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The Beacon schema for genomic allows 3 options: * VRS MolecularVariation * VRS SystemicVariation * Beacon LegacyVariation (which adopts the VRS location object but uses separate definitions otherwise) Unfortunately, during Beacon v2 approval only VRS 1.2. was available and then explicitly referenced in the schema. It fast superseded by 1.3 which allows a *much* better definition of "Systemic Variations" such as CNV. This PR changes all VRS references from 1.2 => 1.3 and should be very welcome to implementers (1.3. has been the longstanding standard now until the future 2.x is out; in fact, the `bycon` based implementations such as progenetix.org have been using it for their Beacons for ~2years).
The `beacon_yaml2md.pl` doc generator contains hard coded definitions to VRS 1.2 `CopyNumber` which doesn't exist in 1.3. This should be fixed separately, possibly w/ revision of the schema documentation method/engine.
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This is an addition to the VRS schema link fix, bumping the version. Reasoning:
The Beacon schema for genomic allows 3 options:
Unfortunately, during Beacon v2 approval only VRS 1.2. was available and then explicitly referenced in the schema. It fast superseded by 1.3 which allows a much better definition of "Systemic Variations" such as CNV.
This PR changes all VRS references from 1.2 => 1.3 and should be very welcome to implementers (1.3. has been the longstanding standard now until the future 2.x is out; in fact, the
byconbased implementations such as progenetix.org have been using it for their Beacons for ~2years).