Release v1.3.0

We're excited to announce the v1.3.0 release of JBrowse Web! Some highlights of
this release include:

In-app plugin store

Building on the plugin store on our website in the last release, we're now
excited to announce that plugins can be installed from within JBrowse Web!
Plugins from our plugin store can now be installed with the click of a button.

Open local files

JBrowse Web now has the ability for tracks to use files on your local hard
drive. This is a great option if you want to visualize files you have locally
without uploading them to a server. These files will need to be re-opened each
time the app is opened or refreshed, but more robust handling of local files
will be available when we release JBrowse Desktop.

Color by MM and MP/ML tags in BAM/CRAM

The MM and MP/ML tags can be used to color alignments tracks by either base
modifications or by methylation. The modifications mode is exciting because it
can show arbitrary DNA/RNA modifications, and the methylation mode uses
specific CpG context to show both modified and unmodified CpGs.

In this screenshot, the top alignments track is colored by methylation and the
bottom alignments track is colored by base modification.

1.3.0 (2021-05-24)

Packages in this release

Package	Download
@jbrowse/core	https://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-tools	https://www.npmjs.com/package/@jbrowse/development-tools
@jbrowse/plugin-alignments	https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view	https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config	https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management	https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-gff3	https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse
@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-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence	https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg	https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@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-linear-genome-view	https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

🚀 Enhancement

• Other
  • #2001 Make tracks added using the add track widget a session track if not in adminMode (@cmdcolin)
  • #1980 Add popup confirmation dialog for unknown session plugins, and use plugins.json as a whitelist (@cmdcolin)
  • #1977 Upgrade @material-ui/data-grid (@cmdcolin)
• core
  • #1982 Allow manually specifying adapter type if filename does not match expected pattern (@cmdcolin)
  • #1975 Allow local files on the users computer to be opened as tracks in jbrowse-web (@cmdcolin)
  • #1865 Show modified bases using MM and MP/ML tags in BAM/CRAM (@cmdcolin)
  • #1984 Better feature details when there are short arrays of json supplied as feature data (@cmdcolin)
  • #1931 Create in app graphical plugin store (@elliothershberg)

🐛 Bug Fix

• core
  • #1985 Avoid error calculating UTR on features that have no exon subfeatures (@cmdcolin)
  • #1954 Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering (@cmdcolin)
  • #1963 Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components (@cmdcolin)
  • #1945 Fix hic not being able to render due to incorrect lazy loading (@cmdcolin)
• Other
  • #1956 Fix connection behavior (@garrettjstevens)
  • #1966 Fix ability to use add-track force on symlink tracks (@cmdcolin)
  • #1951 Fix breakpoint split view demo configuration on website (@cmdcolin)

📝 Documentation

• #2002 Add @jbrowse/img to homepage (@cmdcolin)
• #2007 Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details (@cmdcolin)
• #1976 reorganize the demo page to emphasize the cancer sv demo more (@rbuels)
• #1952 Add demo for 1000 genomes extended trio dataset to website (@cmdcolin)
• #1862 Add example for using a build-time included plugin to storybook (@cmdcolin)

🏠 Internal

• Other
  • #2003 Make SNPCoverage independently generate the modifications tag-color mapping (@cmdcolin)
• core, development-tools
  • #1930 Upgrade react scripts+react to latest versions (@cmdcolin)

Committers: 4

• Colin Diesh (@cmdcolin)
• Elliot Hershberg (@elliothershberg)
• Garrett Stevens (@garrettjstevens)
• Robert Buels (@rbuels)