marade

Perhaps the datasets tested for this were insufficiently large. With nearly 1000 genomes in the 6-7Mb range, I'm finding count_overlaps to be quite slow and really wish it would use...

To be more precise, I'm feeding count_overlaps about 8.85 million intervals that range over about 35000 contigs. This is a real life use case. If properly implemented, wouldn't multiple cores...

Ah, it seems my query is timely. pyranges v0 was still going after 18 hours on that dataset, so I've switched over and restarted. It's still crunching after a few...

It's still going after 24 hours, and I'm still getting a lot of those warning messages. I wonder if I could take any steps to defragment before running count_overlaps, or...

FYI, I abandoned that run after a few days. While it was running, I was able to write a Rust program using rust_lapper and the cov method: https://docs.rs/rust-lapper/latest/rust_lapper/ https://docs.rs/rust-lapper/latest/rust_lapper/struct.Lapper.html#method.cov That...

Sure thing. It's quite simple, using tab-delimited Minimap2 outputs for the intervals. This code is simplified a little bit to keep it easy to read: ``` ranges = {} for...

Here's another candidate: https://www.biorxiv.org/content/10.1101/2024.07.05.602086v1 https://github.com/BioinformaticsLabAtMUN/BacTermFinder