Filtering VCF by ranges
Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- r
- Domain
- bioinformatics
Research direction
Start by reading filterVcf() and the GenomicFiles reduction approach described in the issue. Clarify how range-based iteration should interact with incremental filtering and functional, side-effect-free processing. Done should include an agreed range-filtering behavior rather than filtering only by yield count.
Written by the indexing model from the issue text.
Description
Would be useful to filter a VCF incrementally by range. Range-based iteration makes sense when e.g. removing duplicates. Right now filterVcf() only works by yield count. The GenomicFiles package makes reduction easier but not necessarily filtering at the file level. At least, side effects are undesirable in that functional framework.
- Dominant language
- R
- Stars
- 32
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
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.
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