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)