fix uncertain insertion

[nokara26]

I fixed ins unknown repeat description.
I referred following format:

• DNA: insertion, delins
• RNA: insertion
• Protein: insertion

@totakke
g.1134_1135ins(100) is older hgvs nomenclature?

[codecov]

Codecov Report

Attention: Patch coverage is 89.18919% with 4 lines in your changes missing coverage. Please review.

Project coverage is 89.05%. Comparing base (2a7d403) to head (e11455b).
Report is 1 commits behind head on master.

Files with missing lines	Patch %	Lines
src/clj_hgvs/mutation.cljc	89.18%	0 Missing and 4 partials ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##           master      #10      +/-   ##
==========================================
+ Coverage   89.03%   89.05%   +0.01%     
==========================================
  Files           5        5              
  Lines        1824     1845      +21     
  Branches      127      129       +2     
==========================================
+ Hits         1624     1643      +19     
  Misses         73       73              
- Partials      127      129       +2     

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[totakke]

g.1134_1135ins(100) is older hgvs nomenclature?

Yes. You can see it in the following archive site.

see Uncertain; when the postion and/or the sequence of an inserted sequence has not been defined, a description may have a format like g.(100_150)ins(25)
https://archive.hgvs-nomenclature.org/recommendations/DNA/variant/insertion/

It got probably deprecated at some point.
I feel like we should add a new repairer (clj-hgvs.repairer) from g.1134_1135ins(100) to g.1134_1135insN[100].

[nokara26]

@totakke
Thank you for reply and review!
I added unknown repeat repairer: 4307618

[totakke]

Thank you so much for following the HGVS specification and preparing a repairer to migrate an old expression. 🙇
I have left a couple of comments, and also please bump the version up to 0.5.0-SNAPSHOT.

[totakke]

The description like insN[100] does not mean repeated sequences. It expresses an uncertain inserted sequence. I feel like replace-uncertain-bases is proper naming.

[nokara26]

fix in this commit: b551792

[totakke]

Though only a reference page of DNA deletion-insertion have an example of uncertain insertion, theoretically, RNA deletion-insertion and protein deletion-insertion can also have the uncertain insertion. Mutalyzer supports delinsn, e.g. https://mutalyzer.nl/normalizer/NM_004006.2:r.2623_2803delinsn. Implementation of the uncertain insertion for only DNA deletion-insertion seems incomplete 🤔

[nokara26]

@totakke
Thank you for review!
I fixed rna and protein indel and support ins-format: 4a0f788
And bump the version up: 36d828d

[totakke]

Perfection! Thank you so much 👍

[federkasten]

Thank you for your review, @totakke! 🙏

I have no additional points to add. Thanks!