Fix #4969 - adress the VCF output of given managed variants

[dnil]

This PR adds a functionality or fixes a bug.

• Fix Managed variants VCF #4969 - specifically the variants mentioned there.

First we confirmed on db that the variants were input as noted in the issue. For the future, this can be adressed in #4972.

Here we ensure that each of

• ALT=""
• REF=""
• ALT = "del" or "ins" (rather than <DEL> or <INS>).
  are converted to sensible values during VCF export.

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

[codecov]

Codecov Report

Attention: Patch coverage is 55.55556% with 4 lines in your changes missing coverage. Please review.

Project coverage is 84.77%. Comparing base (1656c2d) to head (627e4c4).
Report is 2 commits behind head on main.

Files with missing lines	Patch %	Lines
scout/commands/export/variant.py	55.55%	4 Missing ⚠️

Additional details and impacted files

@@            Coverage Diff             @@
##             main    #4973      +/-   ##
==========================================
- Coverage   84.78%   84.77%   -0.02%     
==========================================
  Files         320      320              
  Lines       19340    19348       +8     
==========================================
+ Hits        16398    16402       +4     
- Misses       2942     2946       +4     

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[northwestwitch]

Looks good to me!

[sonarcloud]

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 SonarCloud