Populate MT report with stats from d4 files

[northwestwitch]

This PR adds a functionality or fixes a bug.

• Closes #4836

Testing on cg-vm1 server (Clinical Genomics Stockholm)

**Prepare for testing** 1. Make sure the PR is pushed and available on [Docker Hub](https://hub.docker.com/repository/docker/clinicalgenomics/scout-server-stage) 1. Fist book your testing time using the Pax software available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). The resource you are going to call dibs on is `scout-stage` and the server is `cg-vm1`. 1. `ssh @cg-vm1.scilifelab.se` 1. `sudo -iu hiseq.clinical` 1. `ssh localhost` 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `podman ps` 1. Stop the service with current deployed branch: `systemctl --user stop scout.target` 1. Start the scout service with the branch to test: `systemctl --user start scout@` 1. Make sure the branch is deployed: `systemctl --user status scout.target` 1. After testing is done, repeat procedure at [https://pax.scilifelab.se/](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 @hasta.scilifelab.se` 1. Book your testing time using the Pax software. `us; paxa -u -s hasta -r scout-stage`. You can also use the WSGI Pax app available at [https://pax.scilifelab.se/](https://pax.scilifelab.se). 1. (optional) Find out which scout branch is currently deployed on cg-vm1: `conda activate S_scout; pip freeze | grep scout-browser` 1. Deploy the branch to test: `bash /home/proj/production/servers/resources/hasta.scilifelab.se/update-tool-stage.sh -e S_scout -t scout -b ` 1. Make sure the branch is deployed: `us; scout --version` 1. 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. Go to case safeguinea and download the MT report. Make sure it contains the MT vs Autosomes stats

Expected outcome: The functionality should be working Take a screenshot and attach or copy/paste the output.

Review:

• [x] code approved by DN
• [x] tests executed by CR

[codecov[bot]]

Codecov Report

Attention: Patch coverage is 90.62500% with 3 lines in your changes missing coverage. Please review.

Project coverage is 84.58%. Comparing base (63f5f48) to head (0626e8f). Report is 1 commits behind head on main.

Files with missing lines	Patch %	Lines
scout/server/blueprints/cases/controllers.py	66.66%	2 Missing :warning:
scout/server/extensions/chanjo2_extension.py	95.83%	1 Missing :warning:

Additional details and impacted files

```diff @@ Coverage Diff @@ ## main #4850 +/- ## ========================================== + Coverage 84.56% 84.58% +0.01% ========================================== Files 318 319 +1 Lines 19276 19306 +30 ========================================== + Hits 16301 16330 +29 - Misses 2975 2976 +1 ```

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[northwestwitch]

Hi @jemten , I'm working on the MT report using d4 files. I'm testing with a stage case with associated d4 files that I've created from an old bam file that has no MT chrom on it, so on the MT chrom I'm getting coverage 0.

Question: does new d4 files contain MT at all? Are MT stats on another file?

@ramprasadn @rannick

Do we have a recent example of d4 which I can use to test with?

[northwestwitch]

This is ready for review now. I've substituted the d4 file with one that has all chromosomes and it's testable with safeguinea

[sonarcloud[bot]]

Please retry analysis of this Pull-Request directly on SonarCloud