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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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Commits on Nov 16, 2024

  1. VRS references from 1.2 => 1.3 

    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 It fast superseded by 1.3 which allows a *much* better definition of "Systemic Variations" such as CNV.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).
    @mbaudis
    mbaudis committed Nov 16, 2024
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  2. removing the schema deparser changes 

    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.
    @mbaudis
    mbaudis committed Nov 16, 2024
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