Create multi-region arc display type for variant tracks

[cmdcolin]

This adds a new display type LinearPairedArcDisplay, that is main thread rendered, which has generally been useful for creating multi-region displays (hard to do multi-region with the current block based track types)

Summary

• allows BEDPE files to be loaded via jbrowse add-track
• makes BEDPE files of type VariantTrack
• allows user to choose the arc display using the track menu on VariantTrack types
• the LinearPairedArcDisplay render breakends (e.g. <BND>, <TRA>, and long features like <DEL>,<INV>,etc.
• constructs a default tooltip with SV type and feature name
• currently uses SVG, which has nice mouse events, but could potentially consider canvas if we find svg is slow or gets overloaded with large files
• height of arcs automatically adjusts to current display height, similar to LinearReadArcsDisplay

example screenshot on volvox

fixes #3790
fixes #2548 (somewhat fix, this PR makes new display type specific to variant arcs for this, but this may be the most common reason for multi-region arcs)

[cmdcolin]

note that even the regular LinearArcDisplay may benefit from being main-thread multi-region renderer capable. for example, if we do collapse introns, and have a junctions.bed connecting introns, then the arcs will not have 'discontinuities'

[codecov]

Codecov Report

Merging #4045 (b3d77a5) into main (f0063a8) will decrease coverage by 0.40%.
The diff coverage is 16.92%.

@@            Coverage Diff             @@
##             main    #4045      +/-   ##
==========================================
- Coverage   63.63%   63.23%   -0.40%     
==========================================
  Files        1033     1044      +11     
  Lines       30319    30534     +215     
  Branches     7224     7271      +47     
==========================================
+ Hits        19293    19308      +15     
- Misses      10855    11055     +200     
  Partials      171      171              

Files	Coverage Δ
...ins/alignments/src/shared/BaseDisplayComponent.tsx	90.47% <100.00%> (-0.83%)	⬇️
...ins/arc/src/LinearPairedArcDisplay/configSchema.ts	100.00% <100.00%> (ø)
...kpointSplitView/components/BreakpointSplitView.tsx	100.00% <100.00%> (ø)
...plitView/components/BreakpointSplitViewOverlay.tsx	100.00% <100.00%> (ø)
plugins/dotplot-view/src/DotplotReadVsRef/index.ts	100.00% <100.00%> (ø)
...aseLinearDisplay/models/BaseLinearDisplayModel.tsx	85.92% <100.00%> (+0.10%)	⬆️
...me-view/src/BaseLinearDisplay/models/renderSvg.tsx	95.45% <ø> (ø)
plugins/sv-inspector/src/SvInspectorView/index.ts	100.00% <100.00%> (ø)
products/jbrowse-cli/src/commands/add-track.ts	84.21% <100.00%> (+0.22%)	⬆️
products/jbrowse-desktop/src/corePlugins.ts	100.00% <ø> (ø)
... and 14 more

... and 4 files with indirect coverage changes

📣 Codecov offers a browser extension for seamless coverage viewing on GitHub. Try it in Chrome or Firefox today!

[carolinebridge]

Looks really good, don't see any usability issues.

Random thoughts:

• i can't find the ticket, but i'm reminded of an idea suggested awhile back to add tooltips / info / context to certain actions like picking a display type that might not show a helpful view depending on the data provided
• we have "zoom in to see data"... what about "zoom out to see data"? the arc view seems to shine when zoomed all the way out, maybe a prompt to inform the user the visualization might be enhanced if they zoom out? is there a use case for that?
• do we have enough discoverability in our documentation for cross-regional visualizations / data rendering? we've got a ton of support for it at this point might be worth having a dedicated page for it in our user guide

[cmdcolin]

i can't find the ticket, but i'm reminded of an idea suggested awhile back to add tooltips / info / context to certain actions like picking a display type that might not show a helpful view depending on the data provided

yep I think it's #3854 probably still a good endeavor

we have "zoom in to see data"... what about "zoom out to see data"? the arc view seems to shine when zoomed all the way out, maybe a prompt to inform the user the visualization might be enhanced if they zoom out? is there a use case for that?

possibly ya...two sort of related ideas could be a) right clicking an arc, then select "Zoom to feature" (jbrowse 1 actually had a zoom to feature style right click) and b) "Zoom in on the ends of feature in split view" or something like this, where it just creates a multi-region view focused on the ends of the feature, which could help to visualize large deletions or other SVs...

do we have enough discoverability in our documentation for cross-regional visualizations / data rendering? we've got a ton of support for it at this point might be worth having a dedicated page for it in our user guide

yes could be worthwhile, or at least expanding documentation around the features that use this mode

[cmdcolin]

BEDPE tracks were already specified as "VariantTrack" in the "guessTrackType extension point" so the add-track CLI addition is 'copasetic' :)