nf-core / nf-core/variantbenchmarking
vt decompose_blocksub
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enhancement
good first issue
- Dominant language
- Nextflow
- Stars
- 51
- Forks
- 31
- Avg merge
- 1d 22h
- Merged PRs (30d)
- 1
Description
Description of feature
vt decompose_blocksub -a seems to be useful for such cases when variant representation is unusual like:
TTTCGATTTGCAGCAAATTGACTTCTTTAA TA
when such cases exists, trimming prefix or suffix is necessary for normalization.
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
The issue names the vt decompose_blocksub -a command but no repository files or tests. Start by locating where this command is invoked in the pipeline and determine how prefix or suffix trimming should handle the shown unusual representation; done means the case is normalized correctly and covered by a reproducible validation.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100