Releases: GMOD/jbrowse-components
Release v2.6.1
Hello all,
This ended up being a big release with a lot of new stuff!
Features
- 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 createCLI creating corrupted output (update your local install withnpm 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.
🚀 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__mocks__
🐛 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-coreapp-core,core,embedded-coreapp-core
📝 Documentation
- Other
core,embedded-core,product-core
🏠 Internal
app-core,core,product-core,text-indexingcore- Other
app-core,core,product-core,web-coreproduct-coreapp-core,core,embedded-core,product-core,text-indexingcore,product-core
Committers: 6
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Robert Buels (@rbuels)
- Shivang Dwivedi (@studentshivang)
- @Lilas-w Done in 2.84s.
Release v2.5.0
This release includes some small bugfixes. It also renames some internal APIs, if you are a plugin developer, take note of the new naming.
🚀 Enhancement
- Other
core
🐛 Bug Fix
core- #3681 Guard against undefined in CoreGetFeatureDetails (@cmdcolin)
- #3662 Fix empty feature sequence on top-level gene feature (@cmdcolin)
- #3666 Fix text boxes being too small in Dialog boxes (@cmdcolin)
- #3642 Fix error handling of feature detail formatter jexl callbacks (@cmdcolin)
- #3621 Update plugin rollup polyfill package (@garrettjstevens)
- #3620 Fix potential crashes where alignment SEQ field may be empty, simplify some display model code (@cmdcolin)
- Other
- #3670 Only double-click zoom if not clicking on feature (@cmdcolin)
- #3652 Fix text being invisible on overview scalebar when cytobands shown (@cmdcolin)
- #3632 Fix mouse click-and-drag behavior in the alternative "cursor mode" for the dotplot view (@cmdcolin)
- #3625 Fix UCSC trackhub assembly aliases matching (@andrzejgrzelak)
__mocks__,core
📝 Documentation
- Other
core
🏠 Internal
core
Committers: 4
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Robert Buels (@rbuels)
- @andrzejgrzelak
Release v2.4.2
This release addresses a couple small bugs, including a fix for subfeature detail jexl callbacks, spreadsheet view cosmetic improvements, and synteny view mouseovers getting stuck. See details below
🚀 Enhancement
core- Other
- #3586 Add authorization(internetAccount) support for Trix index files (@andrzejgrzelak)
🐛 Bug Fix
- Other
__mocks__,corecore
🏠 Internal
Committers: 2
- Colin Diesh (@cmdcolin)
- @andrzejgrzelak
Release v2.4.1
Hello all, this release adds a number of small enhancements to the dotplot view including scroll zoom, and also fixes a number of small bugs. See the release notes below for details
🚀 Enhancement
core- Other
🐛 Bug Fix
- #3578 Fix selected synteny feature getting unselected after scroll (@cmdcolin)
- #3566 Fix use of "show all regions with data" feature in SV inspector with TRA entries (with CHR2 from INFO) (@cmdcolin)
- #3558 Fix visual effect from using the overview scalebar click and dragging backwards (@cmdcolin)
- #3556 Fix infinite loading state when no synteny features are visible in synteny view (@cmdcolin)
- #3551 Fix bad layout on tabix tracks that have Unicode characters (@cmdcolin)
- #3548 Fix upper case querying of jbrowse 1 text search store (@cmdcolin)
- #3545 Fix issue where clearing search box on LGV import form turns search box into loading bar (@cmdcolin)
📝 Documentation
- #3571 Fixing link to PAG 2023 tutorial (@scottcain)
🏠 Internal
- Other
__mocks__,core,text-indexing
Committers: 2
- Colin Diesh (@cmdcolin)
- Scott Cain (@scottcain)
Release v2.4.0
Hello all! We are excited to announce the new features in this release. Here are some highlights
More theme options and dark mode
The jbrowse web and jbrowse desktop apps now have multiple themes that a user can pick between.
Extra themes can be defined via plugins or via your config file.
See the theme docs for more info and let us know if you have any requests
SVG export of more view types
Dotplot, circular, and linear synteny views have added an SVG export option. The SVG exports can incorporate the current theme, or use a default.
See the changelog below more info
🚀 Enhancement
- Other
core
🐛 Bug Fix
- #3525 Fix missing grid ticks in dotplot (@cmdcolin)
- #3524 Fix loading session shares that have a plus sign in the sessionId (@cmdcolin)
📝 Documentation
Committers: 2
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Release v2.3.4
Hello all,
This release incorporates a "faceted track selector" similar to JBrowse 1. This track selector is available by default as an alternative to the hierarchical selector, to give users the "best of both worlds"
The faceted selector is a dialog box that is opened from a button "Open faceted selector" at the top of the hierarchical selector.
There are a couple other important bugfixes relating to horizontal flipping in the synteny view, and selecting features in the synteny view.
We really enjoyed meeting everyone at PAG 2023 and hearing all the feedback everyone had! We hope to continue rolling out more improvements over the coming year :)
🚀 Enhancement
core- #3494 Use transitionDuration 0 as defaultProp in theme for both popovers and menus (@cmdcolin)
- #3488 Render HTML in faceted track selector for track data/metadata (@cmdcolin)
- #3483 Add anchorOrigin/transformOrigin to default menu component (@cmdcolin)
- #3470 Variant sample grid auto-size columns and resizer (@cmdcolin)
- Other
- #3304 Faceted/data grid style track selector (@cmdcolin)
- #3477 Larger margins to add track workflow to visually clarify next button behavior (@cmdcolin)
- #3475 Bypass plugins.json download if unneeded during app startup (@cmdcolin)
- #3458 Improve auto-update of sequence track height when toggling forward/reverse/translation settings (@cmdcolin)
🐛 Bug Fix
core- Other
📝 Documentation
Committers: 1
- Colin Diesh (@cmdcolin)
Release v2.3.3
Hello all,
This release refactored a number of things with the synteny view that should improve performance. This refactoring also enabled self-vs-self alignments to be rendered by the linear synteny view which previously was not supported.
We also fixed the desktop app not being able to auto-update in v2.2.2-v2.3.2. If you are on one of these versions for JBrowse Desktop, please manually download this release to get back into the auto-update stream :)
🚀 Enhancement
core
🐛 Bug Fix
- Other
core
📝 Documentation
- #3448 Typescriptify some docusaurus website code (@cmdcolin)
- #3444 Human vs mouse synteny demo (@cmdcolin)
🏠 Internal
core
Committers: 1
- Colin Diesh (@cmdcolin)
Release v2.3.2
This release contains important fixes for drawing base-level synteny based on CIGAR strings, especially in inverted regions. We also fixed refName renaming (e.g. your BAM file has 'chr1' but the FASTA has '1') on the new arc display (see v2.3.1).
Additionally, it offers the ability to reverse/complement the sequence in the "Get sequence" dialog.
Screenshot showing how insertions from relative to one assembly exactly match up at a "deletion" relative to another, using the LGV synteny display and curved arcs. Previous versions had bugs but will now match exactly.
Screenshot showing the reverse and complement checkboxes in the Get sequence dialog
🚀 Enhancement
core- Other
🐛 Bug Fix
- #3419 Fix rendering base-level alignments on synteny visualizations, especially in inverted regions (@cmdcolin)
- #3416 Fix rendering alignment arcs on files that need refname renaming and add jitter setting (@cmdcolin)
- #3415 Fix circular view being rendered as a blank area if tab is opened in the background (@cmdcolin)
Committers: 1
- Colin Diesh (@cmdcolin)
Release v2.3.1
Hello all! This release adds some great new features!
-
New "arc" and "read cloud" alignments track modes which render long range
connections between read pairs/split reads. These views have a big impact on
being able to visualize structural variants. -
We now automatically optimize the "prefix size" for our trix indexes created
byjbrowse text-indexwhich should help solve issues with slow text
searching. -
We now refer to many pluggable elements by a "display name" instead of the
coded class name so we have instead of "LinearGCContentDisplay" -> "GC content
display".
New alignments track displays
We created a new display mode that changes the "pileup" of reads into "arcs"
which connects both paired-end reads and split-long read alignments.
New track menu showing the ability to replace the "lower panel" with arc display
or read cloud display
The arc view and read cloud view rendering across discontinuous displayedRegions
A zoomed in view of long-reads (top) and paired-end reads (bottom) at the
breakpoint of a large deletion
Easily toggleable "compact" view of alignments
We now have an easily toggleable compact setting on alignments tracks
(previously had to manually change feature height)
Optimized prefix size for text search indexing
Previously, if indexing long gene IDs with jbrowse text-index it would often
be slow because the "trix" format is generally optimized for short gene symbols.
We added the --prefixSize parameter in previous jbrowse versions to allow
optimizing for specific gene ID lengths, but this was sort of a magic number. Now,
jbrowse text-index will automatically calculate the --prefixSize if none is
provided, which tries to get an even ~64kb bin size. Let us know how it goes for
your data!
Re-install the CLI tools with e.g. npm install -g @jbrowse/cli to get the
latest version with this feature.
Moved "Track Hub Registry" plugin to plugin store
We removed the "Track Hub Registry" plugin, which was previously a "core
plugin", to the plugin store. This will allow us to update the plugin over time
and respond better to issues when they change their remote API.
See release notes below for details
🚀 Enhancement
- Other
coretext-indexing
🐛 Bug Fix
- Other
- #3407 Remove trackhub registry plugin from core plugins, moved to plugin store (@cmdcolin)
- #3406 Fix loading connection tracks from connections that don't specify assemblyNames in config (@cmdcolin)
- #3390 Fix positioning within large alignments for query->target LGV synteny navigation (@cmdcolin)
- #3388 Fix search result that matches synonyms that matches multiple locations (@cmdcolin)
core
📝 Documentation
core- Other
🏠 Internal
__mocks__,core,text-indexingcore
Committers: 1
- Colin Diesh (@cmdcolin)
Release v2.2.2
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.
🚀 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 upgradeCLI 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
📝 Documentation
🏠 Internal
coretext-indexing