DReichLab / DReichLab/ADNA-Tools
Picard MarkDuplicates barcodes
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- Dominant language
- Java
- Stars
- 30
- Forks
- 5
- PR merge metrics
- No merged PRs in 30d
Description
New (3+?) versions of Picard MarkDuplicates limit the character set for barcodes.
--BARCODE_TAG UMIs must match the regular expression ^[ATCGNatcgn-]*$.
If we continue including fragment length, this needs to be encoded in this character set.
Contributor guide
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First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
Research direction
Start by locating the Picard MarkDuplicates invocation and the code that constructs UMIs or includes fragment length. Check how the resulting barcode is passed as BARCODE_TAG, then verify that fragment-length information remains while every value matches Picard's ^[ATCGNatcgn-]*$ constraint.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- java
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 3/5
- Estimated time
- 1-2 days
- Activity status
- Quiet
- Clarity
- Mostly clear
- Newbie friendliness
- 48/100