Seth

The assignments / barcodes are also wrong. Here's the corrected results in rust: ```rust let barcodes_per_sample = vec![ if omit_failing_reads || omit_control_reads { vec![b"AAAAAAAAGATTACAGT".as_slice()] } else { vec![SAMPLE_BARCODE_1, b"AAAAAAAAGATTACAGT".as_slice()] },...

## Analysis ### Overview of existing implementations: **HTSJDK** - factory based object creation - anything using `getSequenceDict` / `getSequence` will error if no index is present - method based for...

Excellent points. I think I'm on board with all of them: 0. The only thing I don't love about this is that presumably every time I ask for `refSeq("chr1")` the...

I can work on this 👍

Looks like this was actually fixed in https://github.com/erg-lang/erg/commit/c79fcd5dbeb6d0b4308ec72fff3f7c9611746309

I'll looking into making this more natively supported. There is also the `--bed-format` option which, with `-z` should make the output more BED like. The output order is currently dictated...

In doing this, be able to support some form of random downsampling. instead of just having a max depth cutoff.

This will likely be happening for the next big release, in conjunction with in-depth mode since the ability to reach inside the pileup engine for metrics will remove a whole...

@25shmeckles - I'm sorry I never replied to this / only just saw it! This is a very cool idea that I would be on-board with. I'm not sure when...

Hello! I've been working on a tool to hopefully mitigate this issue / make it less painful to publish rust tools on conda-forge. It can be found [here](https://github.com/sstadick/cargo-bundle-licenses). In short,...