Release v2.14.0

This release adds some significant new features

• Alignments track 'Group by' functionality: this features allows you to split an alignments track by a specific tag such as RG or HP into multiple new session tracks
• A new adapter type to display sequence names from NCBI FASTA file such as NC_000001.10 in the user interface as chr1. This specifically targets the NCBI "sequence_report.tsv" format to do this renaming, and is called NcbiSequenceReportAliasAdapter

Example screenshot after applying the new Alignments track "Group by" functionality to group by the HP (haplotype) tag. Note that technically, each group is launched as a separate new "session track"

🚀 Enhancement

• core
  • #4532 De-duplicate snackbar messages (@cmdcolin)
  • #4516 Add NCBI sequence_report.tsv alias adapter, with ability to recode NCBI fasta files to use UCSC style names (@cmdcolin)
• Other
  • #4533 Allow setting sequenceType='pep' in ReferenceSequenceTrack configuration (@cmdcolin)
  • #4531 Add UnindexedFastaAdapter for fetching small plaintext FASTA files (@cmdcolin)
  • #4528 Add description config slot to reference sequence track (@cmdcolin)
• app-core, core
  • #4523 Allow plaintext GTF and VCF files greater than 512Mb (@cmdcolin)
• core, product-core
  • #4519 Add "Group by" method for alignments tracks (@cmdcolin)

🐛 Bug Fix

• #4535 Fix crash after navToLocString in some cases (@cmdcolin)

🏠 Internal

• Other
  • #4530 Consolidate gff3 adapter featureData routine, avoid Number-ifying null phase (@cmdcolin)
• core
  • #4518 Don't send displayModel to "rendering" components on server side (@cmdcolin)
• __mocks__, app-core, core, embedded-core, product-core, text-indexing, web-core
  • #4513 Add new eslint rules (no-unnecessary-condition, no-unused-expressions, etc) and tsconfig noUncheckedIndexedAccess (@cmdcolin)
• app-core, core, embedded-core, product-core, text-indexing, web-core
  • #4510 Add biome lint fixes (@cmdcolin)
• core, product-core, text-indexing
  • #4508 Use @mui/x-charts-vendor for d3 upgrade (@cmdcolin)

Committers: 2

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

Release v2.13.1

Fixes bug that caused the track selector in the linear synteny view to be unable to open in v2.13.0

Also allows users to hide the track "outlines" in the linear genome view as an aesthetic preference

without track outlines

with track outlines, and menu item to toggle it

🚀 Enhancement

• #4497 Add ability to toggle "Show track outlines" (@cmdcolin)

🐛 Bug Fix

• #4501 Fix opening track selector in linear synteny view causing crash in v2.13.0 (@cmdcolin)
• #4495 Fix log scale for some types of signal tracks (@cmdcolin)

Committers: 1

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

Release v2.13.0

This release adds the ability to see the assembly name on each row of the synteny view, and adds a number of other small fixes

Example screenshot showing the assembly names on the far left for each row of a synteny view

🚀 Enhancement

• #4494 Add assembly name to scalebar in synteny views (@cmdcolin)
• #4480 Changes default height for SVG rendering to maxHeight to fix blank track effect on slow CPU (@carolinebridge)
• #4478 Add ability to use CSI indexes in @jbrowse/img (@cmdcolin)

🐛 Bug Fix

• core
  • #4483 Fix configuration settings for track sorting in the track selector (@cmdcolin)
• Other
  • #4476 Fix config editor crash in vite usage of embedded components in dev mode (@cmdcolin)
  • #4473 Fix 'Show no tracks active button' checkbox not working (@cmdcolin)

📝 Documentation

• core
  • #4481 Add SARS-CoV2 demo to test_data (@cmdcolin)
• Other
  • #4487 Update faq.md with compression explanation (@Maarten-vd-Sande)

🏠 Internal

• core
  • #4493 Remove prop-types from re-exports (@cmdcolin)
  • #4492 Change abortable-promise-cache to @gmod/abortable-promise-cache (@cmdcolin)
• Other
  • #4488 Fix autogen docs build (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge)
• Colin Diesh (@cmdcolin)
• @Maarten-vd-Sande Done in 1.66s.

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.