~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).

Added

Changed

Fixed

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

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Expected test outcome

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Review

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• "Merge and deploy" approved by
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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

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