Angie Hinrichs

Thanks for the reports @shay671! > DV.8 is seemed to evolve out of DV.1 and not from it’s parent CH.1.1.1 I hope to have this fixed in the 2023-07-06 build....

Sorry, I accidentally hit the 'Comment' button before I was done composing the previous note, so if you're reading these in email, please see the updated comment above: https://github.com/yatisht/usher/issues/345#issuecomment-1624097309

I'm not sure command line would be faster since It takes over two minutes just to read and parse the full tree protobuf. **Would an Omicron-only tree (7.6 million samples...

Alternatively, I could make a reduced version of the tree by sample collection date. Currently 98.5% of samples in the full tree have full YYYY-MM-DD dates. If I take the...

Yeah, you're right as usual. 😄 @russcd this would make it possible for the default view of a subtree to be [this](https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/usher-297.subtree1.json?c=pango_lineage_usher&f_userOrOld=uploaded%20sample) instead of the [current default](https://nextstrain.org/fetch/hgwdev.gi.ucsc.edu/~angie/usher-297.subtree1.json). And the downsampled...

OK, this is on the test server. (It came just after the release cutoff so while the performance improvements should be on the main site later today, these changes will...

Hi @Sanyukta2001, I don't think we have a single command to do that, but I think it could be done by extracting VCF from your protobuf tree file, filtering the...

Looks like the UCSC Genome Browser website had a transient error. That kind of error is unrelated to anything in this repo. If it happens again, please email [email protected] so...

Ah, thanks @joverlee521 and @jameshadfield! I wish I'd thought to check the console. OK, I will update the ORF1ab coords in the JSON to list the segments. My code has...

I just downloaded Italy/PIE_IRCC_15895021/2023|EPI_ISL_18331235|2023-09-24 and aligned it to the reference. I believe its base 1882 corresponds to reference base 1889, and I see a 'Y' there (C or T), so...