D4 full coverage

[Jakob37]

Description and reviewer info

What is changed? How does this update improve the pipeline? (For reviewers) How to test it?

Type of change

• [ ] Documentation
• [x] Patch
• [ ] Minor change
• [ ] Major change

Checklist

• [x] Self-review of my code
• [x] Update the CHANGELOG
• [ ] Tag the latest commit (vX.Y.Z format)
• [x] Log samples used for testing in the Verification_samples_log Excel sheet

Documentation

• [ ] At least one other person has reviewed my changes (not required for trivial changes)

Patch

• [ ] Stub run completes without errors or new warnings
• [ ] At least one other person has reviewed and approved my code (not required for trivial changes)

Major / Minor change

• [x] Stub run completes without errors or new warnings
• [x] onco run finishes without any new warnings/errors and the results can be loaded into scout
• [x] wgs single run finishes without any new warnings/errors and the results can be loaded into scout
• [x] wgs trio run finishes without any new warnings/errors and the results can be loaded into scout
• [ ] At least one other person has reviewed and approved my code
• [x] I have made corresponding changes to the documentation (software versions, etc.)

Test/review documentation

Review performed by

• [ ] Alexander
• [ ] Jakob
• [ ] Paul
• [ ] Ryan
• [x] Viktor

(Add if missing)

Testing performed by

• [ ] Alexander
• [x] Jakob
• [ ] Paul
• [ ] Ryan
• [ ] Viktor

[Jakob37]

LGTM!

Thanks! I'll delay merging this though until I have further investigated the issue with the d4 format.

I opened an issue here https://github.com/38/d4-format/issues/78