Comments (4)
That number only affects the building of the index, not the alignment itself. So changing this will not have too much effect. That said, it shouldn't be hardcoded to '8'. Chopper will, at the moment, when a contaminant is being filtered out, not use multithreading. The reason behind this is because it does not support using rayon. This may change in the future, and pull requests are appreciated.
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I'd be happy to give it a crack though I've never worked with rust. I see rayon is the parallelism library. Any tips before I attempt this?
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Well it shouldn't be done with rayon in this case, as that is not supported for minimap2-rs alignment. There are other options for parallelization, but none that I am sufficiently comfortable with.
from chopper.
Here is an example for parallelization
https://github.com/jguhlin/minimap2-rs/blob/main/fakeminimap2/src/main.rs
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Related Issues (20)
- sequencing_summary.txt feature HOT 1
- error: Found argument 'file.fastq' which wasn't expected, or isn't valid in this context HOT 8
- /lib64/libc.so.6 issue HOT 5
- Filter out reads marked as contaminants? HOT 1
- Cannot Download Chopper HOT 4
- Nanopore barcode/adapter detection HOT 2
- missing ".with_cigar()" in Aligner? HOT 7
- Recommended defaults? HOT 5
- Issue in Installation HOT 7
- Not running on aarch64 HOT 11
- Not working on M2 Mac HOT 6
- Help with --contam parameter HOT 1
- chopper with bam files HOT 1
- Instatlation issue HOT 2
- confuse problem HOT 10
- minimap2 preset for `--contam` HOT 9
- chopper v0.8.0 GLIBC_2.XX not found HOT 2
- Cannot use either wget, conda, or mamba to install chopper HOT 7
- --contam :Filter contaminants against a fasta
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