~200x compounds speedup for VCFs with large variants

[fellen31]

Description

The scoring and sorting of a Nallo clinical SV VCF takes ~5 seconds. Thereafter, ~15 minutes is spent on printing the variants to the output file. This PR replaces print_variant() with cat to make that process take two seconds.

Additionally, I ran into some Multiprocessing errors. Replacing Manager with Queue and then closing results seems to do the trick (LLM suggestion). Turning off logging to stderr by default to reduce noice in e.g. pytest.

Changed

• Compounds print_variant() to use cat which provides significant speedups for large variants
• Logging to use standard hierarchy instead of stderr
• Multiprocessing Manager to Queue in score compounds

How to prepare for test

• Ssh to relevant server (depending on type of change)
• Use stage: us
• Paxa the environment: paxa
• Install on stage (example for Hasta):

  bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_[TOOL]-t [TOOL] -b [THIS-BRANCH-NAME] -a

How to test

• Do ...

Expected test outcome

• Check that ...
• Take a screenshot and attach or copy/paste the output.

Review

• Tests executed by
• "Merge and deploy" approved by
  Thanks for filling in who performed the code review and the test!

This version is a

• MAJOR - when you make incompatible API changes
• MINOR - when you add functionality in a backwards compatible manner
• PATCH - when you make backwards compatible bug fixes or documentation/instructions

Implementation Plan

• Document in ...
• Deploy this branch on ...
• Inform to ...

[dnil]

Well found, well worth looking into: that priority concept feels very much an-old-research-and-development-idea-we-dont-use, doesn't it?

[fellen31]

Well found, well worth looking into: that priority concept feels very much an-old-research-and-development-idea-we-dont-use, doesn't it?

Not sure I understand what you mean by priority concept?