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Brackets missing in HGVS Protein description #417

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stolpeo opened this issue Mar 28, 2024 · 1 comment
Open

Brackets missing in HGVS Protein description #417

stolpeo opened this issue Mar 28, 2024 · 1 comment
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@stolpeo
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stolpeo commented Mar 28, 2024

Describe the bug
Brackets are gone for any protein position. As these are predictions they need to be there according to HGVS nomenclature

To Reproduce
Steps to reproduce the behavior:

  1. Go to AnyCase
  2. Look at any Variant
  3. See error eg. p.I2067V

Expected behavior
There needs to be a bracket eg. p.(I2067V)
Carefull "p.?" is written without brackets, e.g. SpliceSiteVariants

Additional context
(https://hgvs-nomenclature.org/stable/background/simple/)](https://hgvs-nomenclature.org/stable/background/simple/#dna-rna-protein)

issue should be fixed in mehari, not in varfish varfish-org/varfish-server#1435

@xiamaz
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xiamaz commented Mar 28, 2024

Design considerations

As Varfish performs no hgvs validation, proper formatting and presentation of hgvs strings should be fully handled by mehari.

For different use-cases people might prefer different styles of presentation of hgvs-strings, but default behavior should as faithfully follow official hgvs guidelines as possible.

@xiamaz xiamaz moved this to Ready in Release Planning Mar 28, 2024
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