Report reverse-complement alignments
Open
Nobody has claimed this yet.
enhancement
- Dominant language
- Python
- Stars
- 5
- Forks
- 4
- Avg merge
- 10h 7m
- Merged PRs (30d)
- 5
Description
Currently, if CFEIntact detects genes that align as reverse-complements to the reference, it reports this as Scrable error.
Then, for that sample, the regions.csv is not very useful because it only tries to align the genes in the forward direction.
This depends on #22
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 reviewing issue #22 and tracing how CFEIntact handles genes that align as reverse-complements and how it generates regions.csv. Confirm the existing Scrable error path and alignment direction handling. Done means reverse-complement alignments are reported correctly and regions.csv remains useful for those samples.
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