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.

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)