Feel free to contribute

[johanneskoester]

Rust-Bio-Tools (RBT) provide command line utilities for small Bioinformatics tasks that are currently either not available elsewhere or either not fast or reliably implemented.

Everybody is welcome to contribute. Please post here if you want me to add you to the team.

@rust-bio/contributors: check this out :-). Do you have something to add as well?

[winni2k]

I recently put together this streaming pileup tool for single-cell data (https://pypi.org/project/streaming-pileupy/). It's pure python right now and fairly slow. It could be sped up using pysam, but I was wondering if rewriting it in rust would provide any further gains above what the pysam API could offer?

[sitag]

@winni2k I have found pysam pretty slow especially if the bam file is massive. htsjdk goes faster by an order of magnitude. rust-htslib is faster still, more importantly massive gains on memory usage.

[mikecuoco]

Hi @johanneskoester and team, I've been learning Rust over the holidays and came across this great repo! I'd love to contribute. I've been thinking about expanding the depth command with some additional functionality akin to deeptools bamCoverage. Are you following any specific file structure in src?

[dlaehnemann]

Welcome, and happy hacking!

Not sure what you mean by specific file structure, beyond general rust/cargo conventions:
https://doc.rust-lang.org/cargo/guide/project-layout.html
Does that help?

And what you are suggesting would just go into this file, I guess:
https://github.com/rust-bio/rust-bio-tools/blob/master/src/bam/depth.rs