suggestion: use samtools view --uncompressed before piping in bamtools_filter
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enhancement
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Description
Description of the bug
Not really a bug, but I think, if bamtools_filter could be sighlty faster if samtools view was called with --uncompressed instead of -b.
I'm too lazy to test :-P
Command used and terminal output
N/A
Relevant files
N/A
System information
No response
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
Open modules/local/bamtools_filter.nf at line 32 and inspect how samtools view is invoked before the pipe. Compare the proposed --uncompressed option with the current -b behavior, then verify that the filtering workflow still produces valid output and that the change improves or preserves performance.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Refactor
- Difficulty
- 1/5
- Estimated time
- Under an hour
- Activity status
- Stale
- Clarity
- Clearly specified
- Newbie friendliness
- 35/100