Fail for contamination at yellow coverage
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
Chanson asked that we not fail a sample for a tiny amount of contamination, such as ten read pairs. We're going to try using the same rules for on-target and off-target scores. If the region was off-target, but it has coverage of at least 50 at all key positions, then it should fail the sample.
- Fail a sample for off-target regions with yellow coverage.
- Display any off-target regions that caused a failure, even in clinical mode.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
No files, tests, or entry points are named. Start by locating the coverage classification and sample-failure logic, then find tests for off-target contamination and clinical-mode reporting. Done means tiny contamination does not fail a sample, qualifying yellow off-target coverage does, and the regions causing failure are displayed in clinical mode.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 35/100