@jbrowse/cli - npm Package Versions

2.13.1 (2024-07-31)

:rocket: Enhancement

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

:bug: 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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.13.0

2.13.0 (2024-07-25)

:rocket: 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: 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)

:memo: Documentation

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

:house: 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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.3

2.12.3 (2024-06-27)

:rocket: Enhancement

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

:bug: Bug Fix

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

:memo: Documentation

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

Committers: 1

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

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.2

Done in 0.74s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.1

Done in 0.81s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.12.0

2.12.0 (2024-06-20)

:rocket: 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: 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)

:house: 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) Done in 1.71s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.11.2

2.11.2 (2024-06-03)

:rocket: 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: 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) Done in 1.23s.

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.11.1

2.11.1 (2024-05-11)

:rocket: 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: 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) Done in 1.13s.

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.11.0

2.11.0 (2024-04-16)

:rocket: 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: 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.

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.3

2.10.3 (2024-03-06)

:rocket: 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: 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)

:memo: 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.

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.2