Pull in more QC fields from Nextclade

[emmahodcroft]

From discussion in 11/11 dev meeting, we talked about allowing users to have more ways to filter sequences based on QC scores. In particular, since we 'let everything in' we should allow users to then have useful ways to filter out things that may be questionable.

There are many ways we could run with this afterwards, but as a first step, we should bring these fields in.

Current status:

Currently we have pulled in only QC fields that are 'objective' (e.g. counts of missing Nucs) and avoided those that are specific to Nextclade
However these could be not-ideal for getting an overall feel for the quality of a sequence and having one good place to filter out 'bad stuff'

Possible Objectives:

• Pull in some of the 'less-objective' fields from Nextclade (ex: overall QC score)
  • Need a list of possible fields
• Make it clear(er) these are from Nextclade and how they're generated/what they mean
• Make it clear these fields may change over time (ex: a 'bad' seq may become 'good' if it's now recognised correctly as a recombinant rather than an outlier)

[emmahodcroft]

I'd suggest we pull in:

'Overall QC Score'
'Overall QC Status'

The following as statuses (ex: 'good', 'mediocre'):
'Missing Data'
'Mixed Sites'
'Private Mutations'
'Mutation Clusters'
'Frame Shifts'
'Stop codons'

One could additionally have a discussion about whether these should additionally be pulled in as the numeric scores as well (if available - I am not sure if they all have numeric values out of 100 as well?) - it would allow users more fine-grained filtering, but would add more fields to TSV, details page, etc etc.

I'd propose to preface all of these with 'Nextclade' to make it clear where these come from as they aren't purely quantitative.

It would be ideal if we could add some kind of (?) icon mouseover on the sequence details page next to these so that people could read more about how they are calculated and/or link to Nextclade descriptions of how these are generated. (I imagine this could be implemented just as a generic text-box mouseover, and one specifies in a config somewhere what the text should be and whether to include a link, for example). However, this may be a separate PR.