phac-nml/biohansel

Shorten QC messages - remove repeated terms

Closed this issue · 2 comments

Suggested enhancement: edit QC messages to remove repeated terms.
For warnings:
"WARNING: Low Coverage: Low coverage for all tiles (18.200 < 20 expected)" -> change to: "WARNING: Low coverage for all tiles (18.200 < 20 expected)"
For missing tiles:
"FAIL: Missing Tiles Error 1: 11.11% missing tiles; more than 5.00% missing tiles threshold. Low coverage depth (19.1 < 20.0 expected); you may need more WGS data." -> change to: "FAIL: 11.11% missing tiles > 5.00% QC setting. Low coverage depth (19.1 < 20.0 expected); you may need more WGS data."
For mixed samples:
"FAIL: Mixed Sample Error 2: Mixed subtype detected. Positive and negative tiles detected for the same target site "2417681" for subtype "1"." -> change to: "FAIL: Mixed subtype detected. Positive and negative tiles detected for the same target site "2417681" for subtype "1"."

Hi @glabbe! Welcome to GitHub 👋

Thanks for taking the time to create an issue about this. I've created a pull request to fix this issue in #47

I'll get @gcttong to review the code before merging into the development branch and creating a new release of bio_hansel.

Awesome, thanks Peter!