More acmg conflicts warnings

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Warning and reference to Bieseker et al 2024 when using PP1/PP4 and BS4 in ACMG classifications
• Warning to not to use PP4 criterion together with PS2/PM6 in ACMG classifications with reference to the SVI Recommendation for De Novo Criteria (PS2 & PM6)
• closes More ACMG co-use warnings  #5101

Testing on cg-vm1 server (Clinical Genomics Stockholm)

Prepare for testing

1. Make sure the PR is pushed and available on Docker Hub
2. Fist book your testing time using the Pax software available at https://pax.scilifelab.se/. The resource you are going to call dibs on is scout-stage and the server is cg-vm1.
3. ssh <USER.NAME>@cg-vm1.scilifelab.se
4. sudo -iu hiseq.clinical
5. ssh localhost
6. (optional) Find out which scout branch is currently deployed on cg-vm1: podman ps
7. Stop the service with current deployed branch: systemctl --user stop scout.target
8. Start the scout service with the branch to test: systemctl --user start scout@<this_branch>
9. Make sure the branch is deployed: systemctl --user status scout.target
10. After testing is done, repeat procedure at https://pax.scilifelab.se/, which will release the allocated resource (scout-stage) to be used for testing by other users.

Testing on hasta server (Clinical Genomics Stockholm)

Prepare for testing

1. ssh <USER.NAME>@hasta.scilifelab.se
2. Book your testing time using the Pax software. us; paxa -u <user> -s hasta -r scout-stage. You can also use the WSGI Pax app available at https://pax.scilifelab.se/.
3. (optional) Find out which scout branch is currently deployed on cg-vm1: conda activate S_scout; pip freeze | grep scout-browser
4. Deploy the branch to test: bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b <this_branch>
5. Make sure the branch is deployed: us; scout --version
6. After testing is done, repeat the paxa procedure, which will release the allocated resource (scout-stage) to be used for testing by other users.

How to test:

1. how to test it, possibly with real cases/data

Expected outcome:
The functionality should be working
Take a screenshot and attach or copy/paste the output.

Review:

• code approved by
• tests executed by CR

[northwestwitch]

refactored this to a set, so you can have as many conflicts as you want instead of just 2

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 84.44%. Comparing base (f1129c5) to head (e8ff8f6).

Additional details and impacted files

@@           Coverage Diff           @@
##             main    #5188   +/-   ##
=======================================
  Coverage   84.44%   84.44%           
=======================================
  Files         327      327           
  Lines       19807    19807           
=======================================
  Hits        16727    16727           
  Misses       3080     3080           

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[sonarqubecloud]

Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarQube Cloud