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Important
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#########
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- * :ref: `SimpleInterval and SequenceState are deprecated
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- <deprecations>`. They will be removed in VRS 2.0.
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+ * SimpleInterval and SequenceState are deprecated. They will be removed in VRS 2.0.
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Major Changes
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#############
@@ -29,33 +28,33 @@ Major Changes
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contiguous molecule
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* :ref: `SystemicVariation ` refers to variation in the context of a
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system, such as a genome, sample, or homologous chromosomes
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- * :ref: ` UtilityVariation ` classes provide useful representations
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+ * UtilityVariation classes provide useful representations
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for certain technical operations
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* New :ref: `SequenceExpressions <SequenceExpression >` subclasses
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replace SequenceState. Subtypes are:
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- * :ref: ` DerivedSequenceExpression ` , which representations sequence
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+ * DerivedSequenceExpression, which representations sequence
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notionally derived from a SequenceLocation
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- * :ref: ` RepeatedSequenceExpression ` , which represents contiguous
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+ * RepeatedSequenceExpression, which represents contiguous
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repeats of a sequence
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* :ref: `LiteralSequenceExpression `, which
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- wraps a :ref: ` Sequence ` and provides data structure parity with
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+ wraps a Sequence and provides data structure parity with
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other SequenceExpressions
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- * :ref: ` CopyNumber ` , a form of SystemicVariation, represents the
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+ * CopyNumber, a form of SystemicVariation, represents the
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copies of a molecule within a genome, and can be used to express
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concepts such as amplification and copy loss.
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- * :ref: ` Gene ` enables reference to an external definition of a gene,
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+ * Gene enables reference to an external definition of a gene,
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particularly for use as a subject of copy number expressions.
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- * :ref: ` DefiniteRange ` and :ref: ` IndefiniteRange ` represent bounded
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- and half-bounded ranges respectively. A new :ref: ` Number ` type
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+ * DefiniteRange and IndefiniteRange represent bounded
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+ and half-bounded ranges respectively. A new Number type
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wraps integers so that some attributes may assume values of any of
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these three types.
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Minor Changes
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#############
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- * Sequence strings are now formally defined by a :ref: ` Sequence `
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+ * Sequence strings are now formally defined by a Sequence
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type, which is fundamentally also a string. This change aids
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documentation but has no technical impact.
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