Release v2.2.1

[cmdcolin]

Hello, we are happy to release v2.2.1!

This contains several improvements including

• Ability to display the reference sequence track as a "GC content" track
• Ability to view SyntenyTracks as a plain track on a regular linear genome
  view, and to create synteny views from this

It also contains two important bug fixes

• In v2.2.0 CRAM features did not display mismatches correctly on alignments tracks
• In v2.2.0 the LGV ImportForm froze when changing assemblies that had the same refnames

We recommend upgrading to fix these issues!

Here are some screenshots of the new features in this release as well

screenshot showing the GC content display on the reference sequence track

menu items for opening the GC content

screenshot showing right click on a feature in a SyntenyTrack -> Open synteny
view

screenshot showing large synteny features on a SyntenyTrack in the LGV using a
hg19 vs hg38 chain liftover file

🚀 Enhancement

• Other
  • #3277 Create new "Add track workflow" that allows pasting JSON track configs (@cmdcolin)
  • #3328 Add GC content display type to the reference sequence track (@cmdcolin)
  • #3316 Add LGV typescripting to @jbrowse/react-linear-genome-view (@cmdcolin)
• core
  • #3298 Add authentication plugin to embedded components (@garrettjstevens)
  • #3329 Add ability to minimize/collapse tracks and views and move views up/down in view stack (@cmdcolin)
  • #3308 Add ability to display synteny track in a normal LGV showing regions of synteny as features (@cmdcolin)
  • #3317 Move ErrorBoundary so that tracks/views that have crashed can be closed more easily (@cmdcolin)

🐛 Bug Fix

• Other
  • #3342 Fix CRAM mismatches calculation regression in v2.2.0 (@cmdcolin)
  • #3319 Fix pileup "sort by" setting being lost on zoom level change (@cmdcolin)
• core
  • #3340 Fix linear genome view import form going into infinite loading state changing assemblies with same refnames (@cmdcolin)
  • #3339 Fix force flag for drawing large regions and node-fetch polyfill for node 18 fix in @jbrowse/img (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

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This discussion was created from the release Release v2.2.1.

[cmdcolin]

this release required upgrading target:es2015 or over in tsconfig files of consumers of embedded components. this may be something we can reduce back down to es5 which is the default installed by create-react-app, next, et al. but for now, change your target to es2015

[cmdcolin]

also requires using @types/react 18+