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.
Molecular Variation refers to variation within or of a contiguous molecule
Systemic Variation 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
Literal Sequence Expression, which wraps a Sequence and provides data structure parity with other SequenceExpressions
Copy Number Variation, 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 use as 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.