Release v2.12.3

This is a hotfix release for a bug in desktop that affected v2.12.2 that prevented sessions from being started

🚀 Enhancement

• #4465 Add contig to the default dontRedispatch list for Gff3TabixAdapter (@cmdcolin)
• #4464 Bump generic-filehandle to put URL in error messages (@cmdcolin)

🐛 Bug Fix

• #4469 Fix error launching session on desktop in v2.12.2 (@cmdcolin)

📝 Documentation

• #4466 Add demo of using farm-fe bundler for embedded components (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.30s.

Release v2.12.2

This was a hotfix release to the v2.12.0 release to fix a Buffer is not defined error. See v2.12.0 release notes for more features https://github.com/GMOD/jbrowse-components/releases/v2.12.0

Release v2.12.0

This release includes

• Added ability to show genomic or feature-relative coordinates in the "Show feature sequence" panel
• Any sidebar widget can be popped out into a dialog box, allowing for more room to see the feature details, config editor, and more
• Fixed sandbox error on startup of the linux AppImage on OSs with specific settings like Ubuntu 24
• Added aggregation to BigBedAdapter for bigGenePred type tracks to make grouped gene glyphs (see screenshot)

Before and after showing the aggregation of transcripts on a bigGenePred type track

Example of the coordinates display on the feature sequence with the dialog

🚀 Enhancement

• Other
  • #4459 Allow using keyboard shortcut for devtools in production desktop builds (@cmdcolin)
  • #4455 Add slot.type to configuration editor elements (@cmdcolin)
  • #4427 Add ctrl+wheel scroll to zoom both top and bottom of synteny view (@cmdcolin)
  • #4425 Add ability to dismiss dotplot warnings (@cmdcolin)
  • #4422 Make initial linear synteny view import form submit show all regions by default (@cmdcolin)
• core
  • #4456 Add aggregation to BigBedAdapter to group bigGenePred transcripts (@cmdcolin)
  • #4448 Adds genomic coordinates back into the sequence panel accounting for strand direction (@carolinebridge)
  • #4423 Speed up large displayedRegions sets by converting MST array of Region[] into a types.frozen<IRegion[]> (@cmdcolin)
  • #4399 Allow viewing coordinates in sequence feature display panel (@cmdcolin)
• app-core
  • #4443 Allow drawer widget to be "popped out" into a dialog box (@cmdcolin)
• core, product-core
  • #3992 Add ability to get refNames for a track in the "About track" panel (@cmdcolin)

🐛 Bug Fix

• Other
  • #4458 Fix sandbox error on AppImage startup on certain linux systems (@cmdcolin)
  • #4441 Fix sorting data grid on multi-wiggle 'Edit colors/arrangement' dialog (@cmdcolin)
  • #4439 Fix blank lines in multi-wiggle add track workflow causing crash (@cmdcolin)
  • #4438 Fix cursor:pointer style on an alignments feature detail clickable link (@cmdcolin)
  • #4436 Fix "Open synteny view at this position" when file contains CIGAR X/= operators (@cmdcolin)
  • #4426 Fix side scroll in linear synteny view causing the browser "back" action (@cmdcolin)
  • #4417 Fix error message shown on chromosomes with missing data for plaintext GFF3 (@cmdcolin)
• core
  • #4442 Fix unstable dialog width in "About track" dialog for multi-quantitative tracks (@cmdcolin)

🏠 Internal

• #4445 Update oclif/test and oclif/core (@cmdcolin)
• #4440 Use ref instead of deprecated findDOMNode for draggable dialog (@cmdcolin)
• #4429 Remove normalize-wheel library (@cmdcolin)
• #4400 Remove node-polyfill-webpack-plugin (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge)
• Colin Diesh (@cmdcolin)

Release v2.11.2

This adds the ability for users and admins to configure filters to tracks. Users can edit the filters interactively with a "Edit filters" dialog box in the track menu, allowing them to only show features above a certain score, or of a certain type, etc.

Screenshot showing the "Edit filters" dialog, making only a single feature type visible

There is also an important bugfix for the "Show soft clipping" feature of alignments tracks

🚀 Enhancement

• Other
  • #4406 Allow loading plaintext GFF3 files larger than 512Mb (@cmdcolin)
  • #4398 Adds a context menu option to zoom to a feature (@carolinebridge)
• core
  • #4405 Include a raw version of function names in error message stack traces (@cmdcolin)
  • #4393 Allow users to configure filters and set them at runtime via a editable dialog (@cmdcolin)
  • #4395 Remove x-data-grid resize bar workaround (@cmdcolin)
  • #4389 Improve return type of intersection2 (@garrettjstevens)

🐛 Bug Fix

• #4407 Fix custom theme being applied in renderings in desktop (@cmdcolin)
• #4402 Fix for rendering of softclipping when there are insertions in the sequence (@cmdcolin)
• #4385 Fix ability to choose line plot bigwig coloring (@cmdcolin)
• #4386 Fix ability to add custom frame colors (@garrettjstevens)

Committers: 3

• Caroline Bridge (@carolinebridge)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

Release v2.11.1

Hello all,
This release fixes a couple of bugs:

• fixed alpha channel compatibility with SVG exports in inkscape/illustrator
• fixed an issue where bookmarks would show up or crash due to loading on the incorrect assembly, and more
• improved remembering of the state of the collapsed categories in the track selector using localStorage

Screenshot of fixed alpha channel from exported SVGs that improves usage with Inkscape/Adobe Illustrator

🚀 Enhancement

• core
  • #4354 Allow capitalizing CDS sequences and lowercasing introns in sequence feature panel (@cmdcolin)
• Other
  • #4351 Store and retrieve user track selector settings in local storage (@cmdcolin)

🐛 Bug Fix

• core
  • #4381 Replace all rgba(...) color strings with rgb(...) in SVG exports to fix usage in illustrator/inkscape (@cmdcolin)
  • #4364 Fix tooltips creating a scrollbar when overflowing off the screen in Chrome (@cmdcolin)
• Other
  • #4366 Fix for regex sequence search on reverse strand features (@cmdcolin)
  • #4362 Auto-detect file format better when importing BED or TSV bookmarks (@cmdcolin)
  • #4357 Fix bookmark showing up on wrong assembly/crashing (@cmdcolin)
  • #4353 Remove snap package (@cmdcolin)
• app-core
  • #4350 Fix Fab positioning on @jbrowse/react-app (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

Release v2.11.0

This release adds a new option "Color by CDS" to color the reference sequence track and CDS features in gene tracks by their reading frame

Screenshot showing the "Color by CDS" setting on the linear genome view menu

This release also adds new Hi-C coloring options, including a log-scale mode that enhances visible patterns

There are also many other small fixes including the ability to highlight multiple regions from the URL bar &highlight= option, faster zooming with the zoom in/out buttons, and more

See release notes for details

2.11.0 (2024-04-16)

🚀 Enhancement

• core
  • #4341 Improve error dialog stack trace display and fix usage on https sites (@cmdcolin)
  • #4340 Change email on error message dialog (@cmdcolin)
  • #4288 Create GCContentTrack type (@cmdcolin)
  • #4312 Update @mui/x-data-grid 6->7 (@cmdcolin)
  • #4280 Add JSON.parse utility to the "jexl function library" (@cmdcolin)
  • #4276 Add retry method to share link dialog in case of error (@cmdcolin)
  • #4266 Add bookmark highlight to overview scale bar (@carolinebridge-oicr)
• Other
  • #4335 Add ability to create multiple highlights on the linear genome view (@carolinebridge-oicr)
  • #4287 Fix snap package and also add deb package (@cmdcolin)
  • #4034 Subtler minicontrols focus (@cmdcolin)
• app-core, product-core
  • #4337 Allow moving tracks and views up/down/to top/to bottom, and better click and drag track re-ordering (@cmdcolin)
• core, product-core
  • #4336 Add new Hi-C color schemes with log scale mode (@cmdcolin)
• core, web-core
  • #4284 Allow getting stack trace error dialog from session.notify errors (@cmdcolin)

🐛 Bug Fix

• Other
  • #4318 Use node-fetch-native to fix warning from JBrowse CLI on node 21+ (@cmdcolin)
  • #4319 Fix Hi-C rendering for some high resolution files (@cmdcolin)
  • #4314 Fix loading of BED12 data from a plaintext BED with column headers (@cmdcolin)
  • #4293 Fix alignment curves showing up in inkscape for breakpoint svg (@cmdcolin)
  • #4287 Fix snap package and also add deb package (@cmdcolin)
  • #4277 Fix usage of --assemblyNames in jbrowse add-connection (@cmdcolin)
  • #4275 Fixes bug on URL highlight param in which refName aliases were not working (@carolinebridge-oicr)
• text-indexing
  • #4269 Avoid crash on badly encoded GFF attributes (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.85s.

Release v2.10.3

This release adds the ability to highlight regions on the linear genome view.

Users can specify a highlight via the URL when they use jbrowse-web, in a format like &loc=chr1:1-1000&assembly=hg19&highlight=chr1:1-100 (it must be used with the &loc and &assembly)

This release also fixes the ability to load BAM and CRAM files where the refName contains a colon

2.10.3 (2024-03-06)

🚀 Enhancement

• Other
  • #4257 Smaller sequence track size (@cmdcolin)
  • #4256 Update deps including electron 28->29 (@cmdcolin)
  • #4234 Adds URL query param for highlight on LGV (@carolinebridge-oicr)
• core, product-core
  • #4255 Allow getting stack trace from track errors (@cmdcolin)

🐛 Bug Fix

• #4254 Throw if no sequenceAdapter supplied to CramAdapter (@cmdcolin)
• #4250 Fix the viewport calculations for when URL params includes &tracklist=true (@cmdcolin)
• #4232 Fix for missing INFO.STRANDS tag for TRA features in breakpoint split view (@cmdcolin)
• #4224 Fix parsing of BAM and CRAM refNames that contain a colon (@cmdcolin)

📝 Documentation

• #4240 Small fixes to embedding tutorial docs (@kwentine)
• #4223 Add FAQ section about faceted track selector (@Maarten-vd-Sande)

Committers: 5

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Quentin Agren (@kwentine)
• @Maarten-vd-Sande Done in 1.56s.

Release v2.10.2

Hello all,
I'm happy to announce v2.10.2

Here are some highlights of this release

Get stack traces from error messages

This release adds a new feature to allow getting the stack trace from error messages, which will show the exact line of code the error occurred on and will help with debugging error reports.

Launch breakpoint split view from alignment feature details

Previously, you could launch a breakpoint split view from a TRA/breakend type feature in the variant feature details, but this allows you to do it directly via a read

Screenshot showing the workflow to launch a breakpoint split view from a read

@jbrowse/img tool fixes

The jb2export command line image exporter from @jbrowse/img had issues with node.js preventing it from running, so this was fixed, and a new ability to export just snpcov visualizations was added. Example

jb2export --bam file.bam snpcov height:400 --fasta hg19.fa --out output.png

2.10.2 (2024-02-19)

🚀 Enhancement

• Other
  • #4219 Add ability to render only snpcoverage in jbrowse-img (@cmdcolin)
  • #4196 Allow adding &tracklist=true to URL bar to open the track selector, &nav=false to hide linear genome view header (@cmdcolin)
• core
  • #4215 Launch breakpoint split view directly from alignments feature details (@cmdcolin)
  • #4184 Add ability to get stack trace for error messages in the UI (@cmdcolin)

🐛 Bug Fix

• Other
  • #4220 Fix hydration error from translocation features in plaintext VCF adapter (@cmdcolin)
  • #4217 Fix breakpoint split view SVG export occasionally having wrong clipping (@cmdcolin)
  • #4213 Fix issue with tagFilter * in alignments track (@cmdcolin)
  • #4208 Fix @jbrowse/img under node environment (@cmdcolin)
  • #4146 Remove --tracks and --view options from set-default-session CLI (@cmdcolin)
• core
  • #4190 Remove text selection on sequence track with user-select: none (@cmdcolin)
• core, product-core
  • #4177 Fix session tracks being displayed in the tracklist on @jbrowse/react-linear-genome-view (@cmdcolin)

📝 Documentation

• #4166 Year in review blog post (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

Release v2.10.1

This is a bugfix release, fixing some issues with svg export and faceted track selector. It also enables directional feet to be drawn on breakend style VCF tracks in the linear genome view with the arc display.

🚀 Enhancement

• core
  • #4155 Remove react-svg-tooltip library (@cmdcolin)
• Other
  • #4152 Add directional feet to breakends in linear arc display (@cmdcolin)
  • #4143 Add webpack build for @jbrowse/react-app (@cmdcolin)

🐛 Bug Fix

• Other
  • #4158 Fix subfeature refNames on BED and BEDTabix parsers (@cmdcolin)
  • #4154 Fix metadata facet filters being blank (@cmdcolin)
• core
  • #4147 Fix bad svg output in v2.10.0 in cases where feature names have angle brackets (@cmdcolin)

📝 Documentation

• #4142 Update 03_assemblies.md (@dtdoering)

Committers: 2

• Colin Diesh (@cmdcolin)
• Drew T. Doering (@dtdoering) Done in 3.10s.

Release v2.10.0

New file format for synteny tracks - PIF

This release adds a new synteny file format PIF ("pairwise indexed format"). It is essentially a small transformation of PAF ("pairwise mapping format") that allows querying the format using tabix.

Preparing a new PIF file

To prepare a PIF file, you can use the @jbrowse/cli tool:

Old workflow

minimap target.fa query.fa > query_vs_target.paf
jbrowse add-assembly target.fa
jbrowse add-assembly query.fa
gzip query_vs_target.paf # optionally gzip paf
jbrowse add-track query_vs_target.paf.gz -a query,target

New

minimap target.fa query.fa > query_vs_target.paf
jbrowse add-assembly target.fa
jbrowse add-assembly query.fa
jbrowse make-pif query_vs_target.paf # generates pif in same folder
jbrowse add-track query_vs_target.pif.gz -a query,target

Conceptually, the PIF file is just a tabix file that allows querying the PAF from either the query->target or the target->query.

Note: We have not yet improved the amount of data needed to view whole-genome overviews of the whole genome alignment, but we anticipate looking into this soon

Impact of using PIF vs PAF

This screenshot shows the example impact of loading a synteny track in the linear genome view: the indexed PIF track allows only a small amount of data to be downloaded, and so it is rendered much quicker. The data is exactly the same as a PAF file

Share link for the screenshot above https://jbrowse.org/code/jb2/main/?config=test_data%2Fhs1_vs_mm39%2Fconfig.json&session=share-DMGteXDmT3&password=6TIWA

Other new features in this release

• added ability to create highlighted regions from the bookmark widget
• click-and-drag or wheel side-scroll in the 'synteny area' of the linear synteny view. additionally, right context click on synteny features
• added support for lzma compression in CRAM files (via @gmod/cram@v2.0.0)

🚀 Enhancement

• core
  • #4138 Speed up large FromConfigAdapter usages with alternative adapter id calculation (@cmdcolin)
  • #4114 Improve pluginManager.jexl typescript definition (@cmdcolin)
• Other
  • #4135 Split "recently used tracks" local storage keys by view assemblies (@cmdcolin)
  • #4003 Adds the ability to highlight regions using the bookmarks widget (@carolinebridge-oicr)
  • #4123 Remove session.notify after using the Add track workflow (@cmdcolin)
  • #3859 Add new pairwise indexed PAF adapter format with CLI creation workflow (@cmdcolin)
  • #4109 Allow right clicking synteny features (@cmdcolin)
  • #4110 Scroll both panels of the linear synteny view when side scrolling the middle panel (@cmdcolin)
  • #4108 Convert to floating-ui for tooltips for small speedup (@cmdcolin)
  • #4107 Refactors and bundle size improvements (@cmdcolin)
• app-core, core
  • #4134 Add ability to click and drag synteny area of synteny view to side scroll (@cmdcolin)

🐛 Bug Fix

• Other
  • #4137 Fix dotplot axis ticks going out of bounds (@cmdcolin)
• core
  • #4136 Fix "Export SVG" feature in next 14 (@cmdcolin)
  • #4125 Fix internet accounts not being shown in file selector after page refresh and hide HTTP basic internet accounts (@cmdcolin)
• app-core, embedded-core
  • #4121 Fix view menu checkboxes not responding in some cases (@cmdcolin)

📝 Documentation

• app-core, product-core, web-core
  • #4106 Add links between autogen docs (@cmdcolin)

🏠 Internal

• #4103 Add mastodon account to website links (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin) Done in 2.06s.