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fix: codon deletion right in front of stop codon is not a stop_gained #515

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merged 4 commits into from
Aug 16, 2024

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@tedil tedil commented Aug 15, 2024

This also changes the way conservative is determined; I am not sure whether the end position is in- or exclusive at that point, i.e. if the change here is correct or not.
Edit: should indeed be end_base + 1

@tedil tedil requested a review from holtgrewe August 15, 2024 11:41
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codecov bot commented Aug 15, 2024

Codecov Report

Attention: Patch coverage is 90.90909% with 1 line in your changes missing coverage. Please review.

Project coverage is 73.97%. Comparing base (2431c21) to head (ffdd805).
Report is 5 commits behind head on main.

Files Patch % Lines
src/annotate/seqvars/csq.rs 90.90% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #515      +/-   ##
==========================================
+ Coverage   73.94%   73.97%   +0.03%     
==========================================
  Files          25       25              
  Lines        9656     9665       +9     
==========================================
+ Hits         7140     7150      +10     
+ Misses       2516     2515       -1     

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@tedil tedil changed the title fix: special case 1 codon deletion right in front of stop codon fix: codon deletion right in front of stop codon is not a stop_gained Aug 15, 2024
@tedil tedil marked this pull request as ready for review August 15, 2024 14:53
@tedil tedil enabled auto-merge (squash) August 16, 2024 08:30
@tedil tedil merged commit 48fd896 into main Aug 16, 2024
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@tedil tedil deleted the fix-incorrect-stop-gained-prediction branch August 16, 2024 08:34
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