Allele Normalization

[ahwagner]

We need to refine Allele Normalization in VRS v1.2 to account for various sequence expression types.

The following was discussed in the 5/24/21 VRS call:

• Normalize LiteralSequenceExpression as SequenceState was normalized
• When using a LiteralSequenceExpression within RepeatedSequenceExpression AND a Number value for Count attribute
  • Convert to a LiteralSequenceExpression
• When using a LiteralSequenceExpression within RepeatedSequenceExpression AND a non-Number value for Count attribute
  • Normalization by subunit (suggested but largely undiscussed)
• When using DerivedSequenceExpression (alone or within RepeatedSequenceExpression), return as-is

[ahwagner]

In discussing further with @larrybabb, we believe it is more correct to not translate between expression types. In the case of a RepeatedSequenceExpression, normalization should refine the SequenceLocation to the entire repeated subunit range found in the reference, analogous to the fully-justified normalization for LiteralSequenceExpressions.

[reece]

Totally agree. Normalization should > adjust values but not types