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Implement BP7 VCEP rules #173

Merged
merged 3 commits into from
Aug 27, 2024
Merged

Implement BP7 VCEP rules #173

merged 3 commits into from
Aug 27, 2024

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gromdimon
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Issue:

Description:

  • Added VCEP rules
  • Added unit tests
  • Changed default BP7 implementation!
  • Corrected benchmark script

@gromdimon gromdimon linked an issue Aug 27, 2024 that may be closed by this pull request
@gromdimon gromdimon merged commit 116f0e4 into main Aug 27, 2024
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@gromdimon gromdimon deleted the 172-implement-bp7-vceps branch August 27, 2024 12:11
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codecov bot commented Aug 27, 2024

Codecov Report

Attention: Patch coverage is 90.86538% with 19 lines in your changes missing coverage. Please review.

Project coverage is 86.21%. Comparing base (f8a6a56) to head (36106ab).
Report is 1 commits behind head on main.

Files Patch % Lines
src/vcep/leber_congenital_amaurosis.py 72.22% 5 Missing ⚠️
src/vcep/pku.py 72.22% 5 Missing ⚠️
src/vcep/pulmonary_hypertension.py 64.28% 5 Missing ⚠️
src/criteria/auto_bp7.py 93.10% 2 Missing ⚠️
src/auto_acmg.py 0.00% 1 Missing ⚠️
src/vcep/scid.py 87.50% 1 Missing ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##             main     #173      +/-   ##
==========================================
+ Coverage   85.97%   86.21%   +0.24%     
==========================================
  Files          63       63              
  Lines        3294     3490     +196     
==========================================
+ Hits         2832     3009     +177     
- Misses        462      481      +19     
Files Coverage Δ
src/defs/annonars_variant.py 100.00% <100.00%> (ø)
src/defs/auto_acmg.py 99.57% <100.00%> (+<0.01%) ⬆️
src/defs/auto_pvs1.py 100.00% <ø> (ø)
src/vcep/brain_malformations.py 100.00% <100.00%> (ø)
src/vcep/cardiomyopathy.py 100.00% <100.00%> (ø)
src/vcep/cdh1.py 100.00% <100.00%> (ø)
src/vcep/cerebral_creatine_deficiency_syndromes.py 100.00% <100.00%> (ø)
src/vcep/coagulation_factor_deficiency.py 97.82% <100.00%> (+0.85%) ⬆️
src/vcep/dicer1.py 100.00% <100.00%> (ø)
src/vcep/enigma.py 100.00% <100.00%> (ø)
... and 15 more

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Implement BP7 VCEPs
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