SACGF / SACGF/variantgrid

Biocommon HGVS validation of edit / ranges

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#1,007 2 comments 0 reactions 2 assignees Claimed by @EmmaTudini View on GitHub
Biocommons HGVS HGVS
Dominant language
Python
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30
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3
Avg merge
9h 28m
Merged PRs (30d)
42

Description

We are affected by [this HGVS bug](https://github.com/biocommons/hgvs/issues/279) ie we can import the following as classification HGVS:

NM_001637.3:c.1582_1583G>A

And because we replace outside references with our references, this has HgvsMatchRefAllele.calculated_ref = 'CC'

So it is imported as:

NM_001637.3(AOAH):c.1582_1583delGGinsA

Expected result: Fails validation

I think we should patch VG code in "Switch reference base" section (line 236) of hgvs_converter_biocommons as well as submit a patch to biocommons HGVS

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