1.2

1.2.0

News

• The first manuscript for VRS has been submitted. Please cite https://www.biorxiv.org/content/10.1101/2021.01.15.426843v1.

• Want to get involved? See the VRS Appendix for the many ways that you can inform and contribute to VRS.

Important

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

Major Changes

• New classification of variation types.

  • MolecularVariation refers to variation within or of a contiguous molecule

  • SystemicVariation refers to variation in the context of a system, such as a genome, sample, or homologous chromosomes

  • UtilityVariation 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.

Minor Changes

• Sequence strings are now formally defined by a Sequence type, which is fundamentally also a string. This change aids documentation but has no technical impact.