Reference Length Expression

New in v2

The ReferenceLengthExpression class is new in VRS v2, and was designed as a means for compact encoding of large ambiguous sequence states following VOCA normalization.

Reference length expressions are used for expressing the state of Alleles where normalization results in a state other than an unambiguous indel or complete deletion (where length = 0). This feature allows for compact representation of the sequence as an expression of a reference subsequence that can be expanded or contracted to the designated length to result in the sequence state. See Allele Normalization for more details.

Reference length expressions also allow for the optional expression of the literal sequence derived from the reference in cases where it is convenient to do so.

Definition and Information Model

Note

This data class is at a trial use maturity level and may change in future releases. Maturity levels are described in the GKS Maturity Model.

Computational Definition

An expression of a sequence that is derived from repeating a subsequence of an associated Sequence Location.

GA4GH Digest

Prefix	Inherent
None	[‘length’, ‘repeatSubunitLength’, ‘type’]

Information Model

Some ReferenceLengthExpression attributes are inherited from Sequence Expression.

Field	Flags	Type	Limits	Description
id		string	0..1	The ‘logical’ identifier of the Entity in the system of record, e.g. a UUID. This ‘id’ is unique within a given system, but may or may not be globally unique outside the system. It is used within a system to reference an object from another.
name		string	0..1	A primary name for the entity.
description		string	0..1	A free-text description of the Entity.
aliases	⋮	string	0..m	Alternative name(s) for the Entity.
extensions	⋮	Extension	0..m	A list of extensions to the Entity, that allow for capture of information not directly supported by elements defined in the model.
type		string	1..1	MUST be “ReferenceLengthExpression”
length		integer | Range	1..1	The number of residues in the expressed sequence.
sequence		sequenceString	0..1	the literal Sequence encoded by the Reference Length Expression.
repeatSubunitLength		integer	1..1	The number of residues in the repeat subunit.

Example

{
    "type": "ReferenceLengthExpression",
    "length": 11,
    "repeatSubunitLength": 3,
    "sequence": "CTCCTCCTCCT"
}