griffithlab / griffithlab/pVACtools
Implement a `--ignore-rna-in-tiering` flag
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- Dominant language
- Python
- Stars
- 188
- Forks
- 81
- Avg merge
- 9d 17h
- Merged PRs (30d)
- 6
Description
From https://github.com/griffithlab/pVACtools/issues/643#issuecomment-1349946776:
There should probably also be a flag --ignore-rna-in-tiering(?) that allows for tiering to treat the experiment as if it has no RNA (even if some of those values exist) - this could be useful when the RNA is of really poor quality.
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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 tiering command and its existing handling of RNA values, then inspect any related command-line options and tests. Implement the requested flag so tiering behaves as though no RNA values are available, and verify that tiering with the flag ignores otherwise present RNA data.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 52/100