Potential fix for #515 - Githubissues

PoonLab / covizu

Rapid analysis and visualization of coronavirus genome variation

https://filogeneti.ca/CoVizu/

MIT License

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Potential fix for #515 #519

Closed ArtPoon closed 5 months ago

ArtPoon commented 5 months ago

removed default clock setting to 8e-4;
use XBB sequence as outgroup for rooting XBB tree, see Art for FASTA;
modified build_timetree() to take outgroup as optional arg;
modified retrieve_genomes to load outgroup

GopiGugan commented 5 months ago

Checking to see if changes for #512 caused the Cypress tests to fail:

1) Beadplot components
       Edge Labels:
     CypressError: Timed out retrying after 10000ms: `cy.trigger()` failed because this element:

`<rect x="253.16443017418032" y="38.5[94](https://github.com/PoonLab/covizu/actions/runs/8283189047/job/22665776423#step:3:95)[95](https://github.com/PoonLab/covizu/actions/runs/8283189047/job/22665776423#step:3:96)145631072" width="7" height="10" class="default" cidx="cidx-465" id="id-548" style="fill: rgb(248, 149, 64);"></rect>`

is being covered by another element:

`<div class="tree-beadplot">...</div>`

ArtPoon commented 5 months ago

Checking to see if changes for #512 caused the Cypress tests to fail:

Ok thanks - I was worried that the problem might be the outgroup sequence FASTA file needed to run my changes, but i don't think we're processing any actual data for testing?

GopiGugan commented 5 months ago

Ok thanks - I was worried that the problem might be the outgroup sequence FASTA file needed to run my changes, but i don't think we're processing any actual data for testing?

Yes, we're not processing any data before running the Cypress tests. Looks like Cypress tests failed because it couldn't find a certain element