2.0.0-snapshot.2025-02.4

What's Changed

• GKS core doc mod by @larrybabb in #637

Full Changelog: 2.0.0-snapshot.2025-02.3...2.0.0-snapshot.2025-02.4

2.0.0-snapshot.2025-02.3

What's Changed

• Update gks core 2025 02.3 by @larrybabb in #635

Full Changelog: 2.0.0-snapshot.2025-02.2...2.0.0-snapshot.2025-02.3

2.0.0-snapshot.2025-02.2

pass thru update to gks-core 1.0.0-snapshot.2025-02.2 changes to maturity levels for some classes

Full Changelog: 2.0.0-snapshot.2025-02.1...2.0.0-snapshot.2025-02.2

2.0.0-snapshot.2025-02.1

What's Changed

• Merge 2.0.0 ballot work since PRC

Full Changelog: 2.0.0-ballot.2024-11.3...2.0.0-snapshot.2025-02.1

VRS 2.0.0 Community Review Ballot

This is the ballot pre-release of the VRS 2.0 specification, open for community review following the GA4GH Product Development and Approval process.

Important Links

Documentation: https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/
Release log: https://vrs.ga4gh.org/en/2.0.0-ballot.2024-11/releases/2.0.html
Schemas: https://github.com/ga4gh/vrs/tree/2.0.0-ballot.2024-11.1/schema/vrs/json
Discussion: #605

Full Changelog: 1.3.0...2.0.0-ballot.2024-11.1

2.0.0 GA4GH 12th Plenary Connect Pre-Release

This is a pre-release version prepared for the GA4GH 12th Plenary Connect (2024) in Melbourne, AUS.

All content in this version is at a DRAFT maturity level.

VRS 2.0.0 Trial Use Ballot

The first ballot release for the VRS specification, this ballot covers models under consideration for advancement to trial use in v2.0.0, including:

• Expression
• Allele
• CisPhasedBlock
• CopyNumberCount
• CopyNumberChange
• SequenceLocation
• SequenceReference
• ReferenceLengthExpression
• LengthExpression
• LiteralSequenceExpression
• Range
• Residue
• SequenceString
• Adjacency
• Terminal
• DerivativeMolecule
• TraversalBlock

GA4GH Connect - April 2024

Initial work on the VRS 2.0 draft specification, including:

• Application of maturity model to VRS data classes
• SV support: Adjacency model
• Class refactor: Haplotype / CisPhasedBlock
• GA4GH Digest key support
• Reference Length Expression encoding

1.3.0 Release: Genotype, Copy Changes, and Composed SEs

Release summary

The v1.3.0 release of VRS includes two new systemic variation concepts:

1. the Genotype model for representing all variants present at a given genomic locus
2. the CopyNumberChange model for representing copy number changes from a regional base ploidy

It also includes support for composed sequence expressions, for expressing sequences composed of multiple underlying expressions.

Additional minor changes include cleanup of the allele normalization guidance, haplotype member minimum, and updates to the processing tools (i.e. gks.metaschema) used to build and represent the schema artifacts. This has also enabled explicity class inheritance and explicit declaration of array ordinality for processing computed digests.

What's Changed

• remove ComposedSequenceExpression from 1.2, belongs in 1.3+ by @ahwagner in #380
• relative copy number by @ahwagner in #382
• Update validation models for Copy Number variation by @korikuzma in #383
• Fix Allele state type priority by @jsstevenson in #384
• 386: revise base64url description by @ahwagner in #387
• explain ref agree normalization rules by @reece in #381
• Add default value for types + update readme for using smoketests by @korikuzma in #390
• C & P error fix in CytobandInterval by @mbaudis in #392
• fix: get smoketests to pass by @korikuzma in #402
• VRS Hackathon Genotype draft by @ahwagner in #394
• Update validation models by @korikuzma in #407
• fix: models.yaml to take ordered property in account by @korikuzma in #409
• Add tests to check schema validation in models.yaml (#406) by @korikuzma in #412
• Add tests for ComposedSequenceExpression (#408) by @korikuzma in #413
• 1.2: Add default value for type in schemas, update smoketests readme by @korikuzma in #391
• Issue 404 by @ahwagner in #416
• relative_copy_class -> copy_assessment in CopyNumberChange example by @mbaudis in #419
• v1.3 release candidate by @ahwagner in #418

New Contributors

• @jsstevenson made their first contribution in #384
• @mbaudis made their first contribution in #392

Full Changelog: 1.2.1...1.3.0

Definition reconciliation and metaschema

This patch version release shores up inconsistencies in the JSON Schema and definitions, and adds a single source-of-truth document from which the JSON Schema and .rst documentation is derived.