Try allowing & coloring recombinants

hodcroftlab / covariants

Real-time updates and information about key SARS-CoV-2 variants, plus the scripts that generate this information.

https://covariants.org/

GNU Affero General Public License v3.0

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Try allowing & coloring recombinants #358

Closed emmahodcroft closed 2 years ago

emmahodcroft commented 2 years ago

Three things:

Allows things marked 'recombinant' by Nextclade to be processed
Tries to plot and colour recombinants (that are not otherwise classified, without other plots, or page)
Only allows sequences with coverage >=90% to try and ensure short sequences classified as recomb aren't included

The last one may change some plots, like Austria, where we may have had many S-gene-only seqs coming through.

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emmahodcroft commented 2 years ago

This looks good - one bug - 'recombinants' doesn't show up on the left-hand menu - but is affected by 'select all' and 'deselect all' - probably just need to adjust the logic a little - will make an issue for this after