The sequence location class is a fundamental concept in VRS, and is used to describe every form of :ref:`Variation`, and has stand-alone utility for describing sequence locations in other (non-variation) contexts. This class is used to represent a subsequence of a specified :ref:`SequenceReference`. The reference is typically a chromosome, transcript, or protein sequence.
At least one of the start and end properties MUST be specified in any SequenceLocation instance.
When only one of these properties is specified, this represents an open interval beginning at the specified
coordinate and extending left (when start is null) or right (when end is null).
When there is ambiguity at a coordinate (e.g., when using a SequenceLocation to describe the confidence boundary of a copy number segment), this is specified using the :ref:`Range` class for that coordinate.
New in v2
In VRS v1, the SequenceLocation class had an interval property which contained start and end
attributes. This intermediate object layer has been removed in v2.0, making start and end
top-level properties of the SequenceLocation.
In some variant representation formats (e.g. HGVS, VCF) sequence variants are described by both their "reference" (ref) and "alternate" (alt) alleles. When representing an Allele with VRS v2, it is also possible to describe the ref sequence (derived from the :ref:SequenceReference at the location) using the sequence property.
New in v2
In VRS v1, sequence derived from the reference was not transmitted. This feature was added in VRS v2 due to this common practice in other variant formats.
When representing a linear sequence, it is expected that for a :ref:`Sequence` of length n, 0 ≤ start ≤ end ≤ n
For a circular sequence, 0 ≤ end ≤ start ≤ n is also allowed. In cases where end < start, this represents
a location that spans the circular sequence origin coordinate.
New in v2
The v2 SequenceLocation now also supports circular sequences. The optional circular property of the
:ref:`SequenceReference` class may be set to True or False to explicitly indicate if a reference is
circular, and therefore if 0 ≤ end ≤ start ≤ n is also allowed.
The Sequence Location class refers to coordinates on a :ref:`SequenceReference`; if that sequence represents a coding transcript, then the coordinates refer to the coding transcript, and not a chromosome sequence to which it aligns. VRS intentionally does not allow for start or end values that use an offset system to represent sequence not found on the :ref:`SequenceReference`.
.. TODO:: Describe and add a ref to an intronic variant profile