feature request: ubam support?
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- Dominant language
- Python
- Stars
- 587
- Forks
- 144
- Avg merge
- 2h 37m
- Merged PRs (30d)
- 1
Description
Pretty self-explanatory. We're trying to eliminate the need to process data in fastq format, so it would be terrific if cutadapt could accept ubam input and write ubam output. (We probably don't need the ability to convert fastq to ubam or vice-versa, so mandating ubam in = ubam out would probably be fine, but we wouldn't say no to additional flexibility either.) And if this were implemented, it would be nice to be able to place trimmed sequences or other metadata into sam tags, similar to the current ability to modify fastq read names and/or comments.) Just a suggestion, thanks!
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
No files, tests, or entry points are identified. Start by locating cutadapt's current input/output handling and determining the required uBAM and SAM-tag behavior. Done would mean a defined, tested implementation scope for uBAM input and output, with the optional metadata flexibility resolved.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 20/100