Add ignored regions to projects
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
Some projects have regions where we expect to see coverage, but we don't require it. For example, HIV-PRI will usually see some coverage in HIV-gag from the primers. The HCV project only really requires coverage in NS3, NS5a, and NS5b, but will usually see coverage in core, E1, E2, NS2, NS4a, NS4b, and p7.
- Add a new option to the project region that allows it to be ignored.
- Good coverage there will not fail the sample for contamination.
- Bad coverage there will not fail the sample for bad coverage.
- Ignored regions are not displayed 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
Start by locating the project-region definition and the checks for contamination, bad coverage, and clinical-mode display. Add the ignored-region option and verify that ignored regions do not cause either failure, are excluded from clinical output, and still permit expected coverage without contamination failure.
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
- 38/100