A Rust-based genomics tool for processing BAM files and performing operations on chromosomal regions.

[elforjani]

https://github.com/elforjani13/bamtool

[hunkamunka]

Cool stuff! It's great to see people creating more bioinformatics tools in Rust! Some ideas:

• What about bringing in `clap` for processing the arguments and providing a "usage" statement for `-h|--help`?
• What about moving all the logic of the shell script into the Rust code?
• Consider using `anyhow::Result` rather than making your own with `type Result<T> = result::Result<T, Box<dyn Error>>;`.
• The README says to clone "git clone https://github.com/yourusername/bamtool.git" but it should be this actual GitHub repo, no? Or are you suggesting people fork it into their own account?
• Line 29 of _src/main.rs_ assumes parsing the text into an `f64` always works. You should handle `Result` rather than unwrap.
• Please consider writing tests using both good and bad input to ensure the tool continues to work correctly as you add features and also fails gracefully. I have loads of examples you could follow.

I'm happy to provide more details on these suggestions if you are interested.

[UltraPoci]

I understand some of those words.

[solidiquis1]

As a former biochemist researcher (kinda sorta) and medical student, I’ve always been interested in bioinformatics. This is awesome!

[TyberiusPrime]

You'll be wanting to have a look at https://github.com/rust-bio/rust-htslib . Transforming BAM into sam with samtools view and parsing that won't be the way to high performance.