ngless-toolkit / ngless-toolkit/ngless
`as_reads` should not require that BAM file be sorted
Open
Nobody has claimed this yet.
enhancement
help wanted
- Dominant language
- Rust
- Stars
- 152
- Forks
- 23
- PR merge metrics
- No merged PRs in 30d
Description
The approach at https://standage.github.io/loading-paired-reads-from-position-sorted-bam-files.html should work well.
Contributor guide
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 with the as_reads implementation and the linked guide on loading paired reads from position-sorted BAM files. Trace where BAM ordering is currently required and compare that behavior with the linked approach. Done means as_reads can process BAM input without requiring the file to be sorted, with behavior verified against relevant existing checks.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- rust
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100