@jbrowse/cli - npm Package Versions

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

2.10.2 (2024-02-19)

:rocket: 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: 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)

:memo: Documentation

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

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.42s.

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.1

2.10.1 (2024-01-09)

:rocket: 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: 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)

:memo: Documentation

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

Committers: 2

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

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.10.0

2.10.0 (2023-12-15)

:rocket: 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: 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)

:memo: Documentation

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

:house: Internal

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

Committers: 2

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

yarn run v1.22.19 $ lerna-changelog --silent --silent --next-version 2.9.0