Ensure chrX and X are treated equally

[fellen31]

Description

Closes #132.

Adds a VCF file with chr prefix, and a test to check that models are equal between both files. I don't know that much python/pytest so let me know if the code can be improved.

Added

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Changed

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Fixed

• Fixed wrong models when chromosome X was named chrX and not X.

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 ...

[fellen31]

I don't think I have enough experience with pytest yet @torbjorgen to fully understand how to best solve this. I don't want to make the codebase worse, but I also know this project is not a priority.

Is moving the common functions to a test_utils.py an okay middle way to reduce code duplication without dealing with pytest fixtures?