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Incorrect translation for unaffected stop codon #86

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merged 1 commit into from
Jan 15, 2024

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nokara26
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@nokara26 nokara26 commented Jan 15, 2024

Resolve #83

I added conditional branch that ter-site position is not changed to extension.

@nokara26 nokara26 self-assigned this Jan 15, 2024
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codecov bot commented Jan 15, 2024

Codecov Report

Attention: 21 lines in your changes are missing coverage. Please review.

Comparison is base (56e3a49) 46.45% compared to head (1a892fe) 46.49%.

Files Patch % Lines
src/varity/vcf_to_hgvs/protein.clj 12.50% 21 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master      #86      +/-   ##
==========================================
+ Coverage   46.45%   46.49%   +0.03%     
==========================================
  Files          16       16              
  Lines        2090     2095       +5     
  Branches       70       70              
==========================================
+ Hits          971      974       +3     
- Misses       1049     1051       +2     
  Partials       70       70              

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Comment on lines +434 to +437
[ppos pref palt {:keys [ref-prot-seq alt-prot-seq alt-tx-prot-seq c-ter-adjusted-alt-prot-seq ini-offset]}]
(if (and (not= ppos 1)
(ter-site-same-pos? ref-prot-seq c-ter-adjusted-alt-prot-seq))
(mut/protein-no-effect)
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In this function, I added line 435-437 and moved seq-info destructuring to args .
And I just fixed indent of following lines.

src/varity/vcf_to_hgvs/protein.clj Outdated Show resolved Hide resolved
@nokara26 nokara26 force-pushed the fix/add-ter-site-no-effect-condition branch from f8178d1 to 1a892fe Compare January 15, 2024 03:11
@nokara26 nokara26 merged commit 422574f into master Jan 15, 2024
31 checks passed
@nokara26 nokara26 deleted the fix/add-ter-site-no-effect-condition branch January 15, 2024 03:18
@nokara26 nokara26 mentioned this pull request Jan 15, 2024
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Incorrect translation for unaffected stop codon
2 participants