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Implementation of PS1 criteria #95

Merged
merged 7 commits into from
May 7, 2024
Merged

Implementation of PS1 criteria #95

merged 7 commits into from
May 7, 2024

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gromdimon
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Issue:

Description:

  • Currentrly WIP.

@gromdimon gromdimon linked an issue May 6, 2024 that may be closed by this pull request
Implement PS1 and PM5 criteria #68
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codecov bot commented May 6, 2024 •
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Codecov Report

Attention: Patch coverage is 84.64419% with 41 lines in your changes are missing coverage. Please review.

Project coverage is 80.66%. Comparing base (24fcc7c) to head (7ec38f2).

❗ Current head 7ec38f2 differs from pull request most recent head d47bda2. Consider uploading reports for the commit d47bda2 to get more accurate results

Additional details and impacted files 
@@            Coverage Diff             @@
##             main      #95      +/-   ##
==========================================
+ Coverage   79.91%   80.66%   +0.74%     
==========================================
  Files          17       20       +3     
  Lines        1230     1443     +213     
==========================================
+ Hits          983     1164     +181     
- Misses        247      279      +32
Files Coverage Δ
src/api/dotty.py 87.50% <100.00%> (ø)
src/api/mehari.py 92.30% <100.00%> (ø)
src/cli.py 95.45% <ø> (-0.20%) ⬇️
src/core/config.py 100.00% <100.00%> (ø)
src/defs/annonars_range.py 100.00% <100.00%> (ø)
src/defs/annonars_variant.py 100.00% <100.00%> (ø)
src/defs/auto_acmg.py 100.00% <100.00%> (ø)
src/defs/auto_pvs1.py 100.00% <100.00%> (ø)
src/defs/seqvar.py 75.53% <100.00%> (ø)
src/defs/strucvar.py 90.16% <100.00%> (-0.16%) ⬇️
... and 6 more

@gromdimon gromdimon marked this pull request as ready for review May 7, 2024 15:12
@gromdimon gromdimon merged commit 720ccc9 into main May 7, 2024
3 checks passed
@gromdimon gromdimon deleted the 68-implement-ps1-and-pm5-criteria branch May 22, 2024 13:33
gromdimon added a commit that referenced this pull request Aug 2, 2024
@gromdimon
Implementation of PS1 criteria (#95)
632466d 
* wip

* generalize annonars models

* tests for annonars variant endpoint

* first implementation of PS1 prediction

* add PM5 support

* docs and tests

* wip
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Implement PS1 and PM5 criteria
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@gromdimon