shenwei356 / shenwei356/seqkit
seqkit amplicon only keeps one amplicon
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- Dominant language
- Go
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Description
Hi,
In version 0.15.0 seqkit amplicon only keeps one amplicon (the largest) per primer pair. I don't always care about the largest amplicon.
Would it be possible to implement the feature of keeping all valid amplicons? A bed file with the start and end bases (columns 2 and 3) of all valid pairs would be fantastic. That would permit me to inspect the amplicons and keep the one I want (in my case, the smallest amplicon over a certain threshold).
Thanks
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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 with the seqkit amplicon command and trace how it selects the largest amplicon for each primer pair. Define the behavior for retaining all valid amplicons and producing a BED file with their start and end bases in columns 2 and 3. Done means users can inspect every valid pair and choose a different amplicon.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- go
- Domain
- bioinformatics, cli
- Issue type
- Feature
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Mostly clear
- Newbie friendliness
- 38/100