Clarify semantics of NARefAlt and AARefAlt

[reece]

Originally reported by: Reece Hart (Bitbucket: reece, GitHub: reece)

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hgvs has two core classes, NARefAlt and AARefAlt that are used to represent SNVs, insertions, deletions, and indels. Although these names made sense when hgvs tried to model ref-alt sequences (in the VCF sense), they now really just model the strings that appear after 'del' or 'ins'. It turns out that RefAlt and DelIns models are deceptively similar and subtly different. This issue must resolve whether to use RefAlt modeling and keep the name, or DelIns modeling and change the name (with appropriate transition).

See DelIns RefAlt Google Spreadsheet for a summary of the similarities and differences with these modeling options.

Also, consider whether p. can use the same model (#333).

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• Bitbucket: https://bitbucket.org/biocommons/hgvs/issue/252

[reece]

Original comment by Reece Hart (Bitbucket: reece, GitHub: reece):

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Attaching a patch of preliminary work. This is old and may not be suitable any longer.

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