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v2.2.2 Release

· 2 min read

Hello all, this release contains a bugfix for the circular view and breakpoint split view with "TRA" type features not being displayed. See release notes below for a couple other small bugfixes and enhancements.

Downloads​

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.

2.2.2 (2022-12-06)​

🚀 Enhancement​

  • Other
    • #3350 Retain feature labels in compact display mode for SVG features, and allow keeping feature description without feature label (@cmdcolin)
    • #3357 Allow holding shift key to create rubberband selection on LGV (@cmdcolin)
    • #3363 Create remove-track CLI command (@cmdcolin)
    • #3341 Add BEDPE adapter type (@cmdcolin)
  • core

🐛 Bug Fix​

  • Other
    • #3377 Fix rendering and clicking synteny features when using MainThreadRpc (@cmdcolin)
    • #3375 Fix jbrowse upgrade CLI command overwriting config.json with --branch or --nightly options (@cmdcolin)
    • #3370 Fix error with SNPCoverage not rendering MM tag modifications in some cases (@cmdcolin)
    • #3366 Fix ability to use LGV synteny track on inverted alignments (@cmdcolin)
    • #3348 Fix for breakpoint split view and circular view issues with <TRA> type entries in v2.2.1 (@cmdcolin)
  • core
    • #3369 Fix uncaught promise errors and add lint rule for catching these (@cmdcolin)

📝 Documentation​

🏠 Internal​

  • core
    • #3368 Create base "Dialog" component to standardize dialogs across codebase (@cmdcolin)
  • text-indexing

Committers: 2​

v2.2.1 Release

· 2 min read

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

Downloads​

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.

2.2.1 (2022-11-21)​

🚀 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​

v2.2.0 Release

· 3 min read

This release includes several important improvements including

  • Lazily loading assembly refNames: previously when you had multiple assemblies in your config, it would load all their refNames at browser startup. Now, it only fetches refNames when you request to use an assembly.
  • Simplified "synteny track selector" on the dotplot and synteny import forms
  • Improved documentation! The entire jbrowse 2 documentation has been overhauled, and the monolithic user guide, config guide, and developer guide pages have been split into smaller pages. We also now auto-generate documentation on our config and state tree models, and have a search bar
  • Improved speed on alignments tracks: a small optimization was made for alignments tracks that can improve performance on alignments tracks by 30% or so especially on short reads

Figure showing improved speed on short read alignments of the refactor (this release) vs main (which was v2.1.7)

Note that the changes to allow lazy loading assemblies may have somewhat changed the "contract", so if your code is using the assemblyManager directly in any places, please be aware of this change. Proper usage of the assemblyManager API uses either

  1. use assemblyManager.get(assemblyName) which can return undefined initially, but then this initiates the lazy load and can be caught by reactivity of wrapping your components in observers
  2. use assemblyManager.waitForAssembly(assemblyName) function, which is asynchronous but returns a promise. this avoids the initial return undefined behavior
  3. avoid directly accessing e.g. assemblyManager.assemblies

Downloads​

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.

2.2.0 (2022-11-04)​

🚀 Enhancement​

  • Other
  • core
    • #3299 Add ability to open a synteny track directly from the dotplot/linear synteny view import forms (@cmdcolin)
    • #3287 Lazy-load assemblies on demand instead of all at app startup (@cmdcolin)
    • #3279 Remove unnecessary expanded region query and small refactors (@cmdcolin)

🐛 Bug Fix​

  • core
    • #3309 Fix animated "Loading..." message keyframes (@cmdcolin)
    • #3306 Fix the RefNameAutocomplete displaying a stale value for chromosome names (@cmdcolin)
    • #3302 Improve rubberband zooming across elided regions (@cmdcolin)
  • Other
    • #3293 Fix CRAM plotting for data files that encode insertions in uncommon way (@cmdcolin)

📝 Documentation​

🏠 Internal​

Committers: 3​

v2.1.7 Release

· One min read

This release fixes the build of @jbrowse/react-linear-genome-view under webpack 4, which had trouble due to the web worker support added in v2.1.6

Downloads​

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.

2.1.7 (2022-10-20)​

🐛 Bug Fix​

  • #3282 Fix for embedded build with webpack 4 failing with v2.1.6 (@cmdcolin)

Committers: 1​

v2.1.6 Release

· 4 min read

We are happy to release v2.1.6

This has several important fixes and improvements

  • Tracks no longer hang in "Loading..." state under Safari and Webkit based browsers, a bug with starting the webworker was fixed
  • There is now an option to use the WebWorkerRpc on the @jbrowse/react-linear-genome-view. This is a great improvement because the WebWorkerRpc dramatically reduces the "stalling" of the main thread when large datasets like BAM/CRAM are being loaded. See https://jbrowse.org/storybook/lgv/main/?path=/story/using-webworker-rpc--page for more info!
  • All feature types, not just gene features, can obtain the underlying feature sequence with upstream/downstream options
  • The ability to refer to plugins in a path relative to your data directory has been fixed, so you can easily refer to plugins in your config file with e.g. "plugins":[{"name":"MyPlugin","umdLoc":{"uri":"myplugin.js"}}] (umdLoc resolves the uri relative to the config.json file that it is in use). There is also umdUrl which can be used in place of umdLoc which can be used like this "plugins":[{"name":"MyPlugin","umdUrl":"myplugin.js"}] and this will resolve relative to the jbrowse root directory e.g. where the index.html is. We recommend using UMD for now, as ESM modules do not have full browser support e.g. in firefox yet, but this will likely be changing soon and we will update tutorials when this occurs!

See our volvox example for a simple no-build plugin https://github.com/GMOD/jbrowse-components/blob/main/test_data/volvox/umd_plugin.js along with it's config https://github.com/GMOD/jbrowse-components/blob/main/test_data/volvox/config.json and see our no-build plugin tutorial! https://jbrowse.org/jb2/docs/tutorials/no_build_plugin_tutorial/

Screenshot of the feature sequence panel showing on a SNP, allowing you to get upstream and downstream sequence of the SNP

Downloads​

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.

2.1.6 (2022-10-19)​

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bedhttps://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-viewhttps://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

🚀 Enhancement​

  • Other
    • #3272 Disable resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff (@cmdcolin)
    • #3254 Use tick labels that correspond to the overview's larger zoom level (@cmdcolin)
  • core
    • #3230 Add ability to customize About dialog with callbacks and optionally hide links to data (@cmdcolin)
    • #3275 Add help dialog for feature sequence panel (@cmdcolin)
    • #3250 Handle alternate line endings (@garrettjstevens)
    • #3252 Fix gene sequence fetching in embedded, and allow fetching genomic sequence for other feature types (@cmdcolin)
  • core, text-indexing

🐛 Bug Fix​

📝 Documentation​

🏠 Internal​

Committers: 3​

v2.1.5 Release

· 3 min read

We are happy to present v2.1.5! This release adds the ability for the embedded linear genome view component to have session tracks, and we added a new UI for alerts/errors on tracks. See the changelog for details.

Other issues with the circular genome view, authentication on jbrowse-desktop, and the trackhub registry were also fixed. Enjoy!

Downloads​

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.

2.1.5 (2022-10-03)​

🚀 Enhancement​

  • Other
    • #3200 Use Alert component for track messages (@garrettjstevens)
    • #3229 Allow user to select local assembly to add tracks to for trackhub registry (@cmdcolin)
    • #3220 Improve error reporting on SV inspector/spreadsheet view on import form (@cmdcolin)
    • #3198 Improve error reporting on jbrowse-web start screen when user attempts to open a broken recent session (@carolinebridge-oicr)
  • core
    • #3223 Allow adding session tracks to embedded react component along with disableAddTracks option if unwanted (@cmdcolin)
    • #3227 Add infrastructure for creating linear-genome-view sub-classes (@carolinebridge-oicr)
    • #3215 Add error boundary on view, track, and drawer widget (@cmdcolin)
    • #3216 Add ability to set number of bp to fetch up/down stream/inside intron in feature details (@cmdcolin)

🐛 Bug Fix​

  • Other
    • #3241 Fix local session failing to load copying between tabs in some cases (@cmdcolin)
    • #3234 Fix circular embedded view failing to load in v2.1.3 and v2.1.4 (@cmdcolin)
    • #3233 Fix legend being cutoff on multiwiggle tracks with wide window (@cmdcolin)
    • #3217 Fix loading tracks from connection using assembly alias (@cmdcolin)
    • #3214 Fix trackhub registry failing to load in 2.x.y versions of jbrowse (@cmdcolin)
    • #3204 Fix authentication configuration on jbrowse-desktop (@cmdcolin)
  • core

📝 Documentation​

🏠 Internal​

Committers: 3​

v2.1.4 Release

· One min read

This release fixes the UMD builds for the react components which failed to upload to npm in 2.1.3

Downloads​

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.

2.1.4 (2022-09-16)​

🐛 Bug Fix​

  • #3191 Fix the UMD build of the react embedded components (@cmdcolin)

Committers: 1​

v2.1.3 Release

· 3 min read

This release includes a quality-of-life improvement for users plotting synteny with CIGAR strings. Before this version, the x-axis in the dotplot was assumed to be target sequence (and similarly, the top row in the linear synteny view was assumed to be the target sequence). But now, target can be either x- or y-axis in dotplot, and top or bottom in linear synteny views, removing the need for the user to care as much about query-vs-target ordering.

This release also includes several fixes for the the behavior of text searching in the linear genome view, a new button to open a .jbrowse file directly from the start screen on jbrowse-desktop, and an important bugfix to plotting inverted alignments on dotplots that affected versions v2.1.0-v2.1.2.

Screenshot showing the latest jbrowse desktop start screen, with a button to open .jbrowse sessions

Screenshot showing both X/Y orientations of two yeast genomes on the dotplot view, focusing on the deletions and insertions.

Enjoy!

Downloads​

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.

2.1.3 (2022-09-15)​

🚀 Enhancement​

  • Other
    • #3188 Add 'Open saved session' button to start screen on desktop (@cmdcolin)
    • #3187 Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table (@cmdcolin)
    • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
    • #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
    • #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
    • #3162 Add about dialog with version number for embedded components (@cmdcolin)
    • #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
  • core

🐛 Bug Fix​

  • core
    • #3168 Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form (@cmdcolin)
    • #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
  • Other

📝 Documentation​

🏠 Internal​

Committers: 4​

v2.1.2 Release

· 2 min read

Hello all, we are pleased to announce v2.1.2!

This release includes a number of small bugfixes to the multi-wiggle track type, and a new feature for performing small sequence searches/motifs in the visible region.

Screenshot of the sequence search feature. It is available from the "view menu" on the linear genome view

Also, we just recently published the pre-print for our JBrowse 2 paper on bioRxiv! https://www.biorxiv.org/content/10.1101/2022.07.28.501447v1

This is a tour de force describing the basic ideas behind JBrowse 2 as an app. We are really pleased with how users and developers have helped to contribute to JBrowse 2 thus far, and look forward to many more years!

Downloads​

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​

🐛 Bug Fix​

  • Other
    • #3157 Support the "name" field on multi-wiggle adapter subadapters instead of source (@cmdcolin)
    • #3154 Use the union of all the subadapter refNames for the MultiWiggleAdapter getRefNames (@cmdcolin)
    • #3156 Fix for mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode (@cmdcolin)
    • #3151 Fix ability to click and drag overview scale bar dragging right to left (@cmdcolin)
    • #3133 Update the ref name box when assembly is changed in LGV import form (@garrettjstevens)
    • #3131 Use "code" instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo (@garrettjstevens)
    • #3119 Use es2015 setting for commonjs builds of packages to fix @jbrowse/img (@cmdcolin)
    • #3142 Fix unicode arrow icon not rendering with some fonts in configuration editor (@garrettjstevens)
  • core
    • #3120 Fix menu items for changing display type from track menu (@cmdcolin)

Committers: 2​

v2.1.0 Release

· 3 min read

We are pleased to present 2.1.0! This release adds some significant new features including:

  • Multi-wiggle tracks - This allows, for example, multiple bigwig files to be displayed in a single track with synchronized scalebar settings. See multi-wiggle docs for more info.
  • Undo and redo functionality, let's you undo an operation in the UI e.g. closing a view, closing a track can be recovered
  • An alert when the dotplot view renders features that go beyond the bounds of the selected region. This is often an indication that the wrong assembly is being used or the query and target are backwards

Example links for multi-bigwig sessions

Multi-row plot showing 21 ENCODE bigWig tracks

Overlapping "xyplot" rendering multiwiggle rendering mode with "emphasised" points showing tumor vs normal coverage

Dotplot view showing warnings from rendering dotplot, generally due to the wrong assemblies being compared. Screenshot also shows the dropdown menu to choose whether mouse click-and-drag pans the view or selects a region

Undo and redo buttons in the Tools menu, also accessible from keyboard shortcuts ctrl+z/ctrl+y and cmd+z/cmd+shift+z. The Undo/Redo function is available in jbrowse-web and jbrowse-desktop currently

Downloads​

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.

2.1.0 (2022-07-28)​

🚀 Enhancement​

  • core
    • #3111 Create undo manager in jbrowse-web and jbrowse-desktop (@cmdcolin)
    • #3115 Add warning when dotplot renders outside of it's boundaries, and create click-and-drag panning of dotplot view (@cmdcolin)
    • #3102 Allow creating alternative "add track workflows" from within the "Add track" widget (@cmdcolin)
    • #3043 Create MultiWiggle track type, adapter, and renderers (@cmdcolin)
  • Other
    • #3113 Improve SVG performance by avoiding re-render when feature is clicked (@cmdcolin)
    • #3110 Remove TSDX from plugin development tools (@garrettjstevens)
    • #3106 Add "emphasis" mode for no fill/scatterplot mode in XYPlot type renderings (@cmdcolin)

🐛 Bug Fix​

  • Other
    • #3109 Better support for developing plugins from within yarn 2+ workspaces (include __virtual folder in build) (@garrettjstevens)
  • core

📝 Documentation​

Committers: 2​