ga4gh/vrs: New variation Types, SequenceExpressions, CopyNumber

Deprecations

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

• 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