Release v2.18.0

This release marks a number of improvements including

New multi-variant display modes

• Ability to display multi-sample VCF in a 'matrix' or 'stacked' style view
• Supports both large 1000 genomes style VCF or smaller trio VCF
• Allows users to cluster rows by genotype using a call out to R script

Screenshot of the multi-variant viewer

Major improvements to the spreadsheet and SV inspector views

• Allows opening tracks in the spreadsheet and SV inspector

• Uses @mui/x-data-grid for display of the spreadsheet

• Makes separate columns for VCF INFO fields

• Support larger files by storing data in 'volatile' storage that doesn't bog down the session

• Support DEL, INV, and all types of SVs instead of just TRA and BND type variants in the SV inspector

• Re-navigates existing breakpoint split view instead of launching a new one each time

screenshot showing the new datagrid for the SV inspector

screenshot showing that you can open up tracks in the import form of the SV inspector

Saves user sessions in a local IndexedDB

• Sessions are saved in IndexedDB instead of localStorage which has much higher capacity and organization, so you won't lose your sessions if your web browser closes!
• Users can create "favorite" sessions to revisit for later
• Admins can also create pre-configured sessions for their instancse for users

screenshot showing the new session manager with recent sessions, favorite sessions, and pre-configured sessions

Improved "aborting" behavior

This is an ongoing refactor, but there is now new improved 'aborting' behavior reducing some of the re-calculations that bog down the UI.

Optimized and improved jbrowse-plugin-gwas

• New optimizations added for loading large GWAS style BED datasets to enable better jbrowse-plugin-gwas features
• The jbrowse-plugin-gwas also added a better clickmap allowing you to see the mouse-over feature https://github.com/cmdcolin/jbrowse-plugin-gwas

2.18.0 (2024-12-10)

🚀 Enhancement

• core, product-core, sv-core
  • #4511 Add 'matrix' display for multi-sample VCFs (@cmdcolin)
• Other
  • #4692 Rename some session options on desktop "File" menu (@cmdcolin)
  • #4703 Add mobx transaction to multi-level synteny zoom (@cmdcolin)
  • #4696 BED optimizations for GWAS type data (@cmdcolin)
  • #4693 Add mate.name to LGVSyntenyDisplay feature mouseovers (@cmdcolin)
  • #4694 Allow opening bedpe files from users tracks in SV inspector (@cmdcolin)
  • #4672 Add BedGraphAdapter and BedGraphTabixAdapter (@cmdcolin)
• app-core, core, product-core, web-core
  • #4074 Autosave sessions in jbrowse-web IndexedDB database to make it easier to access old sessions (@cmdcolin)
• app-core, core, embedded-core, product-core, sv-core, text-indexing, web-core
  • #4682 SV inspector improvements (x-data-grid, opening track data, re-navigate breakpoint split view, support INV/DEL/more) (@cmdcolin)
• core, product-core
  • #4178 Add ability to use colorBy and filterBy for alignments track configs, and group by strand (@cmdcolin)
• core, product-core, text-indexing
  • #4663 Replace AbortSignal with "stop token" to rescue some aborting behavior (@cmdcolin)

🐛 Bug Fix

• #4708 Avoid full length sequence fetch on SNP coverage calculation (@cmdcolin)
• #4676 Fix MCScanAnchorsAdapter rendering in linear genome view (@cmdcolin)
• #4670 Fix GC-content track regression in v2.17.0 (@cmdcolin)
• #4667 Reduce self-pairing for some paired-end read data in breakpoint split view (@cmdcolin)

🏠 Internal

• __mocks__, app-core, core, embedded-core, product-core, sv-core, text-indexing, web-core
  • #4680 Add eslint-plugin-import for sort ordering (@cmdcolin)
• Other
  • #4675 Add fix for potential hydration mismatch errors (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.52s.

Release v2.17.0

This release adds:

• Improved and bugfixed rendering of modified bases from BAM/CRAM files, particularly, it matches in many ways the IGV rendering of modified bases [^1]
• Improved performance for ultra-long reads from Nanopore, especially with zooming in and out and scrolling because it caches the mismatches instead of re-calculating them repeatedly [^2]
• Improved performance for wiggle tracks, multi-wiggle tracks, and SNP coverage tracks, particularly changing the height for these track types produces less re-rendering
• A new data adapter loading BLAST tabular -outfmt 6 alignments for the synteny view
• Fixed interpretation of the 'ts' tag from minimap2 for RNA-seq strandedness
• Improved bedMethyl support

figure showing updated modifications rendering, and bedMethyl as a "MultiQuantitativeTrack"

example of the BLAST tabular adapter, showing TBLASTX results

[^1] Importantly, JBrowse 2 now takes into account the ML tag (likelihood) to better report the results when tools are providing low probability modification likelihoods, especially for when there are multiple modification possibilities at each position (e.g. commonly outputted from Dorado which reported as 'm' and 'h' probabilities, we now only choose the highest likelihood for reporting, which is in line with interpretation from the MM/ML tag specification)

[^2] As part of this change, the internals of BAM/CRAM records have been changed. If you have code that was directly accessing any internal attributes of these records, it may not work anymore. Please use the feature.get('...') on features to get data of interest. The .get(...) method is the only "official" API for accessing data on feature objects, and contact us if you run into any problems!

2.17.0 (2024-11-18)

🚀 Enhancement

• core
  • #4662 Add better handling for bedMethyl files (@cmdcolin)
  • #4652 Reduce re-rendering on quantitative and snpcoverage track height adjustments (@cmdcolin)
  • #4651 Add mismatches cache to improve performance on ultra-long reads (@cmdcolin)
• Other
  • #4649 Add support for displaying SNPs in "no_ref" CRAM files (@cmdcolin)
  • #4627 Create BLAST tabular adapter (@garrettjstevens)

🐛 Bug Fix

• Other
  • #4647 Improved rendering of modifications (@cmdcolin)
  • #4646 Fix mouseover pixelation on linear synteny view (@cmdcolin)
• core
  • #4639 Fix RNA-seq stranded arc coloring, change the color of RNA-seq introns, and improve compact rendering (@cmdcolin)
  • #4638 Fix rendering of UCSC repeatmasker BigBed and BED files (@cmdcolin)

🏠 Internal

• core
  • #4648 Run codemod fix for some MUI deprecated props (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.81s.

Release v2.16.1

Hi all,

This is a bugfix release! See notes below

2.16.1 (2024-11-03)

🚀 Enhancement

• app-core, core, product-core, text-indexing
  • #4624 Add utility links to synteny feature details to allow centering a view on a feature (@cmdcolin)
• Other
  • #4628 Allow configuring Hi-C normalization and default resolution multiplier (@cmdcolin)
  • #4619 Add resolutionMultiplier config slot to BigWigAdapter (@cmdcolin)

🐛 Bug Fix

• #4634 Fix opening local files in the multi-wiggle add track selector (@cmdcolin)
• #4633 Fix "Add track" select box not going away after selecting element (@cmdcolin)
• #4632 Standardize modification colors between alignments track coverage and pileup subtracks (@cmdcolin)
• #4631 Fix config description of assembly name ordering for synteny data adapters (@cmdcolin)
• #4630 Fix MM tag modifications from particular BAM file failing to render on the negative strand (@cmdcolin)
• #4626 Fix dark redraw on selected features after vertical resize of the synteny canvas (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.20s.
  Done in 0.54s.

Release v2.16.0

This release adds the long awaited ability to visualize "multi-way" synteny using a "series of pairwise" comparisons!

Screenshot of grape vs peach vs cacao

Example link here
https://jbrowse.org/code/jb2/main/?config=%2Fdemos%2Fplant_synteny_demo%2Fconfig2.json&session=share-OzIsqrPjDb&password=0T2Qs

Setting up multi-way synteny views can be performed from the "import form" or via the URL params. We envision further enhancements to come to improve functionality and ease-of-use of these views also.

Screenshot of the multi-way import form

2.16.0 (2024-10-23)

🚀 Enhancement

• Other
  • #4615 Add configuration of transcriptTypes and containerTypes to the svg feature rendering (@cmdcolin)
• app-core, core
  • #4430 Multi-level synteny rendering (@cmdcolin)

🐛 Bug Fix

• Other
  • #4593 Fix navigating to a refname result that is also indexed in search track index (@cmdcolin)
  • #4612 Fix error with tooltips in embedded components in vite dev mode (@cmdcolin)
  • #4602 Fix decoding of CRAM ML tag (@cmdcolin)
  • #4594 Fix highlight button causing issues clicking underlying track features (@cmdcolin)
  • #4586 Update electron-builder to fix broken desktop builds (@cmdcolin)
• core
  • #4600 Fix check for "hasSubSubfeatures" in svg feature rendering (@cmdcolin)
  • #4590 Fix opening .jbrowse files on desktop (@cmdcolin)

📝 Documentation

• #4607 Add tiberius sample dataset and updated gencode and ncbi GFF gene sets (@cmdcolin)

🏠 Internal

• Other
  • #4607 Add tiberius sample dataset and updated gencode and ncbi GFF gene sets (@cmdcolin)
• app-core, core, embedded-core, product-core, web-core
  • #4606 Remove react-error-boundary (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

Release v2.15.4

Fixes Hi-C files failing to load in v2.15.3 and also fixes text indexing on JBrowse Desktop on Windows machines

2.15.4 (2024-09-20)

🐛 Bug Fix

• Other
  • #4582 Fix text indexing on Windows (@cmdcolin)
• text-indexing
  • #4580 Fix indexing plaintext gff/vcf on desktop (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.22s.

Release v2.15.3

This release (hopefully) fixes the SSL code signing on the Windows version of the jbrowse desktop app. This should help auto-updates work better on Windows

2.15.2 (2024-09-18)

🚀 Enhancement

• #4573 Add pif.gz option to synteny import form (@cmdcolin)

🐛 Bug Fix

• #4571 Fix code signing on the windows for jbrowse desktop (@cmdcolin)
• #4566 Fix handling of "." in VCF ALT field (@cmdcolin)

🏠 Internal

• #4569 Refactor GFF3 parser to avoid returning internal _linehash variable (@cmdcolin)

Committers: 1

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

Release v2.15.1

This release adds a bugfix for slow loading times due to a refname aliases bug

It also adds a new visualization mode for breakpoint split view to show paired read and split read orientations, helping to show things like inversions

🚀 Enhancement

• core, sv-core
  • #4561 Create notion of launching a single-row breakpoint split view (@cmdcolin)
• Other
  • #4556 Add dropdown menu from bookmark label clicks (@cmdcolin)
• core
  • #4554 Fix the ability to sort menu items by priority for CascadingMenu (@cmdcolin)

🐛 Bug Fix

• Other
  • #4560 Fix coloring on circular chord renderings (@cmdcolin)
• core
  • #4553 Fix performance regression since v2.14.0 in assembly loading (@cmdcolin)

🏠 Internal

• core
  • #4548 Create BaseTooltip component in @jbrowse/core/ui (@cmdcolin)
• Other
  • #4547 Avoid stream polyfill for GFF3/GTF parsing (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.16s.

Release v2.15.0

This release has a couple updates

• Update to MUIv6
• Fix bug with BigBed names processing
• Fix bug with e.g. @jbrowse/react-linear-genome-view's view menu appearing incorrectly

🚀 Enhancement

• app-core, core, embedded-core, product-core, text-indexing, web-core
  • #4534 Update to MUI v6 (@cmdcolin)

🐛 Bug Fix

• core, embedded-core
  • #4544 Fix cascading sub menus bug in embedded components in v2.14.0 (@cmdcolin)
• core
  • #4545 Fix BigBed decoding of strings in v2.14.0 (@cmdcolin)
• app-core
  • #4542 Fix alignments track feature details customization (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 0.84s.

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.