cancervariants / cancervariants/variation-normalization

Add support for HGVS insertions of form {pos}_{pos}ins{pos}_{pos}

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#434 1 comment 0 reactions 0 assignees View on GitHub
bug enhancement priority:low
Dominant language
Python
Stars
15
Forks
2
PR merge metrics
No merged PRs in 30d

Description

> NM_004006.2:c.849_850ins858_895
the insertion of a copy of nucleotids c.858 to c.895 between nuclotides c.849 and c.850

from https://varnomen.hgvs.org/recommendations/DNA/variant/insertion/

Our tokenizer provided support for this, but our validator and translator does not support this query. Our service returns an internal server error.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by tracing the existing tokenizer support for HGVS insertions through the validator and translator, then reproduce the example query from the issue against the service. Update the validation and translation path so c.849_850ins858_895 is handled without an internal server error, and verify the service returns the expected normalized result.

Written by the indexing model from the issue text.

Assessment

Tech stack
python
Domain
backend-api-design
Issue type
Bug
Difficulty
3/5
Estimated time
1-2 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
45/100

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