Align deletions after frame shift
Nobody has claimed this yet.
- Dominant language
- Python
- Stars
- 21
- Forks
- 11
- Avg merge
- 12h 5m
- Merged PRs (30d)
- 24
Description
#549 added references for SARS-CoV-2, but they have a strange frame shift part way through one of the gene regions. The code that aligns deletions to codon boundaries doesn't know about that frame shift, so it might report two partial deletions when the deletion is shifted to the wrong reading frame. See if deletions are very rare in SARS-CoV-2 and we can ignore this, or actually fix the deletion shifting.
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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 code that aligns deletions to codon boundaries and inspect how the SARS-CoV-2 gene region from #549 is represented. Check whether deletions are rare enough to ignore the frame shift; otherwise compare shifted deletions and ensure the result does not report two partial deletions for one event.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100