Ricky Magner

Hi @droazen, I tested the changes out locally using VCFs with indices in different cloud buckets, and it works. This is perfect for the applications we have in mind. Thanks!

Thanks for the update. Do you know if DeepVariant is guaranteed not to do this sort of behavior with their new ONT model?

Hi, thanks for the reply. I was using `version development` which I had assumed meant it had at least the 1.1 features (including `None`). I agree using some safety checks...

To bump an old issue: I could take a look at this if you knew of a good Java library method to test whether a directory is `noexec` or not,...

Thanks for sharing the Wiki link which addresses using regenotyping with giraffe. It looks like it requires the input VCF to be phased? Is there a best alternative in the...

Just saw this issue [here](https://github.com/lh3/seqtk/issues/3) but can confirm this still happens on the latest version (r130).

Hi, yes those are good points about the DP tag specifically, but was only using it for demonstrative purposes here to make a simple example. And yes, my annotate command...

Ok, I think I realized what was wrong. It seems the "stable" release for the [docs](https://pomegranate.readthedocs.io/en/stable/HiddenMarkovModel.html) which the pop-up redirects to when visiting the site is out of date and...

Great, hope the docs change helps others in the future. For numpy: yeah I appreciate package requirements are always a bit of a headache so there's probably not a perfect...

This looks great, thanks! I just checked v1.21 and it looks like it has the behavior you report, so something in that release must have fixed this.