Ga4gh-vrs

Deprecations

- SimpleInterval and SequenceState are deprecated. They will be removed in VRS 2.0.

Major Changes

- New classification of variation types.
- Molecular Variation refers to variation within or of a contiguous molecular
- Systemic Variation refers to variation in the context of a system, such as a genome, sample, or homologous chromosomes
- Utility Variation classes provide useful representations for certain technical operations

- New SequenceExpressions subclasses replace SequenceState. Subtypes are:
- DerivedSequenceExpression, which representations sequence notionally derived from a SequenceLocation
- RepeatedSequenceExpression, which represents contiguous repeats of a sequence
- LiteralSequenceExpression, which wraps a Sequence and provides data structure parity with other SequenceExpressions

- CopyNumber, a form of SystemicVariation, represents the copies of a molecule within a genome, and can be used to express concepts such as amplification and copy loss.

- Gene enables reference to an external definition of a gene, particularly for useas a subject of copy number expressions.

- DefiniteRange and IndefiniteRange represent bounded and half-bounded ranges respectively. A new Number type wraps integers so that some attributes may assume values of any of these three types.

For more changes, see the [release notes](https://vrs.ga4gh.org/en/stable/releases/1.2.html)

This patch version makes the following corrections and clarifications:

* Adds the intended ChromosomeLocation prefix to the Computed Identifiers table.
* Revises the Cytoband information model to align with ISCN conventions.
* Updates the Cytoband regex to match the specified model.

See [release notes](https://vr-spec.readthedocs.io/en/1.1/releases.html#id2), which has links to more information.

New classes
* ChromosomeLocation: A region of a chromosomed specified by species and name using cytogenetic naming conventions
* CytobandInterval: A contiguous region specified by chromosomal bands features.
* Haplotype: A set of zero or more Alleles.
* VariationSet: A set of Variation objects.

Other data model changes
* Interval was renamed to SequenceInterval. Interval was an internal class that was never instantiated, so this change should not be visable to users.

Documentation changes
* Added Relationship of VRS to existing standards to describe how VRS relates to other standards.
* Updated Normalization to clarify handling of reference alleles and generalize terminology to apply to all VRS objects.
* Updated current and future schema diagrams.
* Included a discussion of the Release Cycle.

The approved Variation Representation specification of the Global Alliance for Genomics and Health.

Second release candidate for the Variation Representation specification of the Global Alliance for Genomics and Health.

First release candidate for the Variation Representation specification of the Global Alliance for Genomics and Health.