v2.6.1 Release

Hello all, This ended up being a big release with a lot of new stuff!

• Created the @jbrowse/react-app NPM package which effectively makes the jbrowse-web package NPM-installable. This is still new so let us know what you think. See the docs at https://jbrowse.org/storybook/app/main and example usages at https://jbrowse.org/jb2/docs/embedded_components/ (this is pretty new, there may be more updates or changes to come with this package!)
• Improved code sharing across web, desktop, and embedded products (this was a large refactor, if you see any bugs let us know!)
• Improved display of inversions in the read cloud display (see screenshot)
• Fixed persistent issue with jbrowse create CLI creating corrupted output (update your local install with npm install -g @jbrowse/cli)

Figure showing split long reads alignments on the read cloud display spanning an inversion showing forward (red) to reverse (blue) and back to forward again.

Downloads

• v2.6.1

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

🚀 Enhancement

• Other
  • #3743 Create mixin for shared code between LinearWiggleDisplay and MultiWiggleLinearDisplay (@cmdcolin)
  • #3711 Allow synteny data adapters to open files larger than 512Mb (@cmdcolin)
  • #3639 Add button to bookmark in jbrowse-web share dialog (@cmdcolin)
  • #3631 Add BEDPE add track workflow, avoid showing "Add track" when disabled (@carolinebridge-oicr)
  • #3700 Render alignment track arcs instantly after bpPerPx change (@cmdcolin)
  • #3695 Reduce re-drawing on alignments track paired read arcs/cloud display types (@cmdcolin)
• core
  • #3725 Filter tracks that match all view.assemblyNames in multi-assembly track selector modes (@cmdcolin)
  • #3531 Add @jbrowse/react-app embedded component (@cmdcolin)
  • #3653 Evaluate extension point on track config pre-process snapshot (@cmdcolin)
  • #3706 Miscellaneous alignments arc/cloud fixes (@cmdcolin)
  • #3698 Add column resizers to the variant ANN/CSQ panels (@cmdcolin)
• app-core, product-core, web-core
  • #3531 Add @jbrowse/react-app embedded component (@cmdcolin)
• __mocks__
  • #3707 Improved read cloud display for long reads with inversions (@cmdcolin)

🐛 Bug Fix

• core
  • #3749 Avoid re-prompting a user login when refresh token is processed (@cmdcolin)
  • #3572 Add OAuth and HTTP BasicAuth servers for local testing, fix some OAuth flows (@garrettjstevens)
  • #3708 Add removable-media to jbrowse desktop snap (@cmdcolin)
  • #3687 Take into account ML tag when showing MM tag on alignments, misc refactoring (@cmdcolin)
• Other
  • #3747 Fix blank lines in GFF crashing text-index (@cmdcolin)
  • #3739 Fix specifying the assemblyNames config slot on add-connection CLI (@cmdcolin)
  • #3631 Add BEDPE add track workflow, avoid showing "Add track" when disabled (@carolinebridge-oicr)
  • #3667 Fix horizontal flip functionality for Hi-C display (@studentshivang)
  • #3703 Fix rendering error in alignments tracks when filtering by tag in CRAM file (@Lilas-w)
  • #3694 Fix ability to filter certain fields in BAM/CRAM files (@cmdcolin)
  • #3691 Fix breakpoint split view alignment connections not pointing at right position in v2.5.0 (@cmdcolin)
  • #3686 Fix jbrowse create/jbrowse upgrade CLI intermittent failures (@cmdcolin)
• product-core, web-core
  • #3738 Don't throw on UCSC connection containing assemblies not matching connection->assemblyNames config (@cmdcolin)
• app-core, core, embedded-core
  • #3731 Fix view menu going off screen in some cases (@cmdcolin)
• app-core
  • #3713 Fix centering of the ImportForm on SV inspector (@cmdcolin)

📝 Documentation

• Other
  • #3752 Add storybook example for fetching features currently in view (@cmdcolin)
  • #3732 Add JBrowse R shiny app demo (@carolinebridge-oicr)
  • #3693 Remove package table from release blogposts (@cmdcolin)
• core, embedded-core, product-core
  • #3704 Organize autogenerated docs into categories (@cmdcolin)

🏠 Internal

• app-core, core, product-core, text-indexing
  • #3740 Bump electron, proxy-agent, fontsource-roboto, etc. and update SnackbarMessage from typed array to object (@cmdcolin)
• core
  • #3741 Distinguish between SessionWithConnections and SessionWithConnectionEditing (@cmdcolin)
• Other
  • #3734 PileupRenderer refactor (@cmdcolin)
• app-core, core, product-core, web-core
  • #3717 More modularizing of shared app code (@cmdcolin)
• product-core
  • #3709 Silence console warn in CopyAndDelete test (@cmdcolin)
• app-core, core, embedded-core, product-core, text-indexing
  • #3701 Create app-core and embedded-core packages (@cmdcolin)
• core, product-core
  • #3661 Create packages/product-core containing shared code between the various products (@rbuels)

Committers: 6

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Robert Buels (@rbuels)
• Shivang Dwivedi (@studentshivang)
• @Lilas-w Done in 2.84s.