james hadfield
james hadfield
Very similar in spirit to https://github.com/nextstrain/augur/issues/1084. It would be great to fix these bugs as it's not at all obvious that data's been dropped, and so it's hard to gauge...
Ran into this again today, except not with spaces but `)` `test.parse.fasta`: ``` >abc)|USA ATCG ``` `augur parse --sequences test.parse.fasta --output-sequences test.parse.out.fasta --output-metadata test.parse.tsv --fields strain country` ```console ==> test.parse.out.fasta...
> It also sounds like, from commentary in the linked https://github.com/nextstrain/augur/issues/1084 (https://github.com/nextstrain/augur/issues/1084#issuecomment-1298236067 and https://github.com/nextstrain/augur/issues/1084#issuecomment-1298547698) that iqtree is also re-writing identifiers, and it's possible that this initial rewriting was an attempt...
Hi Maria, yes you're correct and this has been on the to-do list for many years, however I don't know when we'll get around to fixing it. (It's not trivial...
> When constructing the phylogenetic tree with augur tree, it always alerts maximum recursion depth reached as a fatal error, even when setting augur_recursion_limit to 100,000,000. What could be the...
> My best guess is some limits were introduced during an Augur version update, or some changes on Augur tree functions. I don't think any changes have been made to...
Hey @kvargha - if you change the scale type to "ordinal" or "continuous" they should be ordered. Currently it looks like it's a categorical scale which is ordered by the...
Ahh gotcha. At the moment [this isn't possible](https://docs.nextstrain.org/projects/auspice/en/stable/advanced-functionality/drag-drop-csv-tsv.html#scale-types) but we could add this pretty easily. One option is to allow column names such as `Age:ordinal`. Alternatively we could probably infer...
> Sadly, entropy panel permanently shoes "data loading" after any interaction with the tree (e.g. clicking on a branch or using filters) This is presumably due to [this conditional](https://github.com/nextstrain/auspice/blob/f9d7ec75da44b5acbf30f7b5c361d3cd46760f7b/src/actions/entropy.js#L17-L23) where...
> Alternatively, do you see an easy way to opt out of this optimization and render the entropy always, as before? You could change the source code to modify the...