james hadfield

Yes! The metadata currently won't tell you anything about internal nodes, but if they were labelled in the tree then you could add extra rows to the metadata (or parse...

As of commit 1c95dcf we don't display gubbins blocks unless there is a tree If you can think of a sensible way to display the blocks without a tree then...

Conversation moved from https://github.com/nextstrain/augur/pull/1281#discussion_r1296156887: Entries in the annotations JSON (except "nuc") correspond to translated CDSs, and are interpreted by Auspice as such. In this context, it makes no sense to...

Hey Jon - yeah that seems like the contig's just being ignored. I have some housekeeping admin to do in Phandango at some point so I'll try to get to...

(1 year later...) The [annotations schema now requires 'nuc' to be present](https://github.com/nextstrain/augur/blob/934fdf49f21a0722c889772efbfb0e0fdfb7d92e/augur/data/schema-annotations.json#L26) (d6246ca052478446f7179e230e842a34f93e4cd4) however neither `augur ancestral` nor `augur translate` validate their outputs. Reading any node-data file (via `NodeDataReader`) with...

> however I think it's sensible to require translate to add a 'nuc' block, which is why I made it a required property As of 1d17699e960d3805a0a586d7ccf3e9a550d53ac9 (in master, but not...

I suspect the issue is similar to #147 - can you double check your strain names in the tree and CSV files are identical?

FYI upgrading to `compression-webpack-plugin@10` causes ``` ERROR in Conflict: Multiple assets emit different content to the same filename .gz ```

For sure @kairstenfay. Here's the steps to reproduce: * load (e.g.) zika (auspice v1 or auspice v2) * pan the map * click "download data" -> "Screenshot (SVG)" * See...

A few observations after looking into this today: **Minor errors in VCF genotype syntax** The `write_VCF_translation` produces VCFs which look like this ``` ##fileformat=VCFv4.2 ##source=NextStrain_Protein_Translation ##FORMAT= #CHROM POS ID REF...