Release v1.3.5

We're excited to announce the v1.3.5 release of JBrowse! Some highlights of this release include:

New embedding build of @jbrowse/react-linear-genome-view

This release adds a new UMD build of our @jbrowse/react-linear-genome-view React component. This build will allow users to use our React Linear Genome View in a website that doesn't otherwise use React. See a tutorial for how to get started using this build:

• https://jbrowse.org/jb2/docs/tutorials/embed_linear_genome_view/01_introduction

A preliminary beta version of this build was used in a tutorial at BOSC2020, and that tutorial was also on our website. If you've used that version, the interface has changed somewhat, so come check out the new tutorial for the official released version!

Bookmark widget

A new widget has been added that is accessible from the Linear Genome View view menu or when you click and drag over a region in the header (a.k.a rubber band selection). This view keeps a list of bookmarked regions, which you can add custom labels to, and also which you can use to navigate back to that region. The bookmarks can also be exported.

Note to plugin developers

If your plugin adds menu items or context menu items to a track, or customizes renderProps, there may be some changes that affect how those menu items work, particularly in #2226 and #2229. Also see an updated example of context menu items here.

1.3.5 (2021-08-23)

Packages in this release

Package	Download
@jbrowse/core	https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments	https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed	https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view	https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-data-management	https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-grid-bookmark	https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view	https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-sequence	https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variants	https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle	https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli	https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-circular-genome-view	https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view	https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

🚀 Enhancement

• Other
  • #2163 Add new embeddable React Circular Genome View (@garrettjstevens)
  • #2229 Use extendPluggableElement for context menu items (@garrettjstevens)
  • #2233 Add optional chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files with many refseqs (@cmdcolin)
  • #2199 Make the BED parser not interpret general tab delimited data as BED12 (@cmdcolin)
  • #2241 Restore previous window location when re-opening on desktop (@garrettjstevens)
  • #2203 Add a helpful message if there is a 404 on config.json error (@cmdcolin)
  • #2204 Hide reads with unmapped flag by default in alignments tracks (@cmdcolin)
  • #2198 Add better inversion visualization to read vs reference visualizations (@cmdcolin)
  • #2154 Add UMD build of react-linear-genome-view for plain-js use (@garrettjstevens)
• core
  • #2236 Detect assembly loading error and encapsulate error instead of failing at app level (@cmdcolin)
  • #2029 Polish desktop builds (@elliothershberg)
  • #2140 New core plugin that adds a "bookmarked regions" list widget, new extension points system (@elliothershberg)

🐛 Bug Fix

• core
  • #2245 Fix missing regenerator runtime dependency in core (@garrettjstevens)
  • #2202 Fixed a crash when an incompatible adapter is selected for provided data in 'open track' (@carolinebridge-oicr)
  • #2197 Fix handle leak for killed worker checker (@cmdcolin)
• Other
  • #2208 Fix issue where collapsed categories were not remembered after toggling a track (@cmdcolin)

📝 Documentation

• #2192 Update Linear Genome View embedding docs (@garrettjstevens)

🏠 Internal

• core
  • #2057 Use idMaker for dataAdapterCache key for faster FromConfigAdapter performance (@cmdcolin)
  • #2231 Export offscreenCanvasUtils (@cmdcolin)
  • #2226 Use superRenderProps and superTrackMenuItems for better simulated inheritance model (@cmdcolin)
  • #1874 Add aborting to CoreGetFeatures rpcManager call (@cmdcolin)
• Other
  • #2232 Remove filtering display type from core (@cmdcolin)
  • #2234 Add rootModel setError on jbrowse-desktop (@cmdcolin)

Committers: 4

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)