james hadfield

This would be advantageous to have for SARS-CoV-2 where there are already overlapping ORFs in nextstrain.org/ncov/global and the situation is even more complex than this, e.g. see Figure 1 from...

Duplicate of #1056 (or, more precisely, #1056 is a duplicate of this)

> Sorry for coming in, just want to ask, does augur translate currently assumes that all CDS in the genbank file are forward strand? Hey @ZarulHanifah -- this is purely...

Ouch, let's get this functionality fixed! (The failing test logs have expired, so I can't see what's wrong there.) I am confused as to how [we do this correctly for...

It's true that there is inconsistency in filtering at the moment, however I believe that the current implementation of genotype filtering is "more truthful" and that the problems lie with...

This would be a good improvement I think. I'm changing labels here, as I believe this behavior was intentional when it was implemented, albeit quite some time ago. I'll note...

It [appears to](https://github.com/nextstrain/auspice/blob/master/src/components/entropy/index.js#L215-L245) try to use gene boundaries for aa mutations, and 5% if nucleotide.

Sporadically I can create out-of-sync behavior when performing actions in quick succession - probably due to issues when you use d3 to manipulate an element while a d3 transition is...

Augur clades neds quite a bit of work under the hood to make it more robust and to consider & document edge-cases in behavior. I wrote a bit about this...

Linking this PR to read about the history of how we got here: https://github.com/nextstrain/auspice/pull/925