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update SeqLoc documentation to discuss sequence attribute
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ahwagner committed Apr 19, 2024
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14 changes: 13 additions & 1 deletion docs/source/concepts/location/SequenceLocation.rst
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Expand Up @@ -28,10 +28,22 @@ of a copy number segment), this is specified using the :ref:`Range` class for th

.. admonition:: New in v2

In VRS v1.x, the ``SequenceLocation`` class had an ``interval`` property which contained ``start`` and ``end``
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``.

The "Ref" Allele
################

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.

.. admonition:: 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.

Linear and Circular Sequence Coordinates
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