Important: This documentation covers Yarn 1 (Classic).
For Yarn 2+ docs and migration guide, see yarnpkg.com.

Package detail

@jbrowse/plugin-gff3

GMOD2.4kApache-2.03.5.1TypeScript support: included

JBrowse 2 gff3.

jbrowse, jbrowse2

readme

Build Status Coverage Status Contributor Covenant

jbrowse-components

Monorepo using Lerna and Yarn workspaces containing many related packages for next-generation JBrowse development.

Homepage https://jbrowse.org/jb2

Docs http://jbrowse.org/jb2/docs/

Fall 2023: New outreach! We created an "office hours" Google Calendar for anyone to schedule 1-on-1 meetings with the development team. Details below:

Pre-requisites

You may need additional pre-requisites on certain versions of nodejs.

On macOS with homebrew:

brew install pkg-config cairo pango libpng jpeg giflib librsvg

On Ubuntu, with apt:

sudo apt install -y python3 make gcc libcairo2-dev libpango1.0-dev libjpeg-dev libgif-dev librsvg2-dev

Install (Linux/Mac)

Simply clone the git repo and run yarn in the root repository

git clone https://github.com/GMOD/jbrowse-components.git
cd jbrowse-components
yarn

Install (Windows)

# Make sure you check out line-endings as-is by running
# `git config --global core.autocrlf false`
# Also, make sure symlinks are enabled by running
# `git config --global core.symlinks true`.
# You may also need to clone as an administrator for symlinks to work.
git clone -c core.symlinks=true https://github.com/GMOD/jbrowse-components.git
cd .\jbrowse-components\
yarn

Quick start for developers

You can use these commands to help get started with your development environment

For running jbrowse-web

cd products/jbrowse-web
yarn start

For jbrowse-desktop, launch two tabs

# starts webpack dev server
cd products/jbrowse-desktop
yarn start

# starts electron window
cd products/jbrowse-desktop
yarn electron

For running e.g. jbrowse-react-linear-genome-view you can use storybook

cd products/jbrowse-react-linear-genome-view
yarn storybook

See CONTRIBUTING.md for more info

If you are installing JBrowse on your server, check out our quick start guides here https://jbrowse.org/jb2/docs/

changelog

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.5.1

3.5.1 (2025-06-05)

:rocket: Enhancement

  • Other
    • #5064 Optimize fetching many small sequences from IndexedFasta (e.g. MSA datasets) (@cmdcolin)
    • #5059 Canonicalize refNames in search results (@cmdcolin)
    • #5056 Use assembly displayName on synteny header and ruler (@garrettjstevens)
    • #5050 Use standard sessionId for linear synteny view to reduce data re-fetching (@cmdcolin)
  • app-core, core, embedded-core
    • #5063 Improve usability of dropdown menus by making submenus not disappear immediately onMouseLeave (@cmdcolin)
  • core
  • app-core, core
    • #5044 Allow plugins to register entries onto the root configuration (@cmdcolin)

:bug: Bug Fix

:memo: Documentation

:house: Internal

  • Other
  • core
    • #5061 Modularize some integration tests for launching views (@cmdcolin)

Committers: 2

yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.5.0

3.5.0 (2025-05-27)

:rocket: Enhancement

  • #5042 Avoid inferring CDS subfeatures from non-coding gene pred features (@cmdcolin)
  • #5035 Use trash icon for uninstall in plugin store, and add version number string (@cmdcolin)
  • #4735 Remove jbrowse-web start screen (@cmdcolin)
  • #5025 Allow hiding insertion and deletion in synteny view to help chain file visualization (@cmdcolin)

:bug: Bug Fix

  • Other
    • #5037 Check that breakpoint split view is ready before fetching to avoid crash/large data fetching (@cmdcolin)
    • #5033 Bump @gmod/bbi to fix loading bigwig files from bigtools (@cmdcolin)
    • #5024 Fix lines crossing over view headers in breakpoint split view by only setting sticky view headers on top-level views (@cmdcolin)
  • core

:house: Internal

  • core
  • Other
    • #5036 Remove the async keyword from BaseLinearDisplayModel (@cmdcolin)

Committers: 2

yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.4.0

3.4.0 (2025-05-13)

:rocket: Enhancement

  • core
    • #5018 Avoid serializing large features to sessions to fix quota exceeded errors in localstorage (@cmdcolin)
    • #5010 Add mouseover metadata for fields in the base feature widget (@cmdcolin)
    • #4998 Add padding to the genomic window of search result hits (@cmdcolin)
    • #4995 Add uFuzzy to improve gene name search (@cmdcolin)
    • #4983 Update some data parser packages for ESM compat (@cmdcolin)
    • #4980 Synthesize displayId if none provided in display config (@cmdcolin)
    • #4972 Support cytoband bed files starting with "#" (@cmdcolin)
  • Other
    • #5008 Allow parsing non-indexed BED files larger than 512MB (@cmdcolin)
    • #4997 Better message for "quota exceeded" message from localstorage (@cmdcolin)
    • #4974 Minor optimizations in multi-sample variant rendering (@cmdcolin)
    • #4973 Add basic cytoband for Drosophila (@cmdcolin)
    • #4970 Dynamically toggle wheel-scroll normalization to improve touchpad pinch-to-zoom usage (@cmdcolin)

:bug: Bug Fix

  • core
    • #5013 Fix UCSC chain parsing which have header lines (@cmdcolin)
    • #4993 Fix re-export of @mui/material/styles, and re-export theme (@cmdcolin)
    • #4968 Fix theme augmentation for primary/secondary colors in v3.3.0 (@cmdcolin)
  • Other
    • #5004 Fix modifications rendering broken in v3.2.0 (@cmdcolin)
    • #4992 Fix mouseover for some variable width bigwig features (@cmdcolin)
    • #4984 Avoid rendering 'yellow' for low scores in wiggle density renderings with 'log-scale' enabled (@cmdcolin)
    • #4969 Avoid aggregating bigbed features with geneName === 'none' (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.3.0

3.3.0 (2025-04-18)

:rocket: Enhancement

:bug: Bug Fix

  • Other
    • #4929 Fix broken bigbed features when there is gene level aggregation (@cmdcolin)
  • core

:memo: Documentation

  • core
    • #4949 Controlling navigation of embedded component - storybook examples (@cmdcolin)
    • #4924 Add config docs for pre-processors with simplified config snapshots (@cmdcolin)
  • Other

:house: Internal

  • core

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.2.0

3.2.0 (2025-03-22)

:rocket: Enhancement

  • core
    • #4919 Add in-app clustering method for multi-wiggle tracks (@cmdcolin)
    • #4909 Add ability to load refNameAliases from chromAliases.bb file (@cmdcolin)
    • #4906 Add in-app clustering method for genotype matrix (@cmdcolin)
  • Other
    • #4914 Allow looking up header column by name for RefNameAliases (@cmdcolin)
    • #4910 Allow refNameColumn in RefNameAliasAdapter to override the default displayed refnames (@cmdcolin)
    • #4907 Simplified snapshot API for initial navigation of LGV (@cmdcolin)
  • app-core, core, product-core, web-core
    • #4899 Add aborting to multi-variant rendering, multi-wiggle rendering (@cmdcolin)

:bug: Bug Fix

  • #4920 Fix issue where multi-level linear synteny view would show a blank tracklist (@cmdcolin)
  • #4913 Fix parent aggregation in BigBed files using larger request window (@cmdcolin)
  • #4905 Fix bug where applying genotype clustering twice produces randomness (@cmdcolin)
  • #4897 Fix clustering for certain sets of bigwig files (@cmdcolin)

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.1.0

3.1.0 (2025-03-14)

:rocket: Enhancement

  • Other
    • #4876 Allow inferring default values of adapter urls to simplify config.json (@cmdcolin)
    • #4875 Add sample data from HGSVCv3 to 1000 genomes demo and config_demo (@cmdcolin)
    • #4880 Allow selecting track error messages with click and drag (@cmdcolin)
    • #4882 Allow clustering multi-wiggle tracks on the fly (@cmdcolin)
    • #4874 Use a '012' matrix to improve clustering of genotypes (@cmdcolin)
  • core
    • #4871 Add deletion, insertion, skip, softclip, hardclip to theme (@cmdcolin)
  • app-core, core, product-core

:bug: Bug Fix

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.5

3.0.5 (2025-03-04)

:bug: Bug Fix

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.4

3.0.4 (2025-03-01)

:rocket: Enhancement

  • Other
  • core
    • #4854 Add status callback for parsing PAF, BLAST tabular, MashMap files (@cmdcolin)

:bug: Bug Fix

  • core
    • #4862 Fix name indexing failure on jbrowse desktop (@cmdcolin)
    • #4851 Fix NCBI sequence aliases refNameAliases adapter for some sequence_report.tsv files (@cmdcolin)
  • Other
    • #4849 Fix height of Hi-C track, and add adjust-to-height (@cmdcolin)
    • #4845 Fix retrieval of VCF metadata for tooltips in VCF feature details (@cmdcolin)
    • #4842 Fix occasional 1px gap in sequence track (@cmdcolin)

:house: Internal

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.3

Done in 0.44s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.2

3.0.2 (2025-02-13)

:rocket: Enhancement

  • core
    • #4834 Update ReExports for @jbrowse/core/BaseFeatureDetails (@cmdcolin)
    • #4818 Improve status updating for BamAdapter, CramAdapter (@cmdcolin)
    • #4811 Improvements to the sesson/config warning dialogs (@cmdcolin)
  • Other
    • #4829 Less gappyness at SVG features block boundaries (@cmdcolin)
    • #4828 Additional ?hubURL compat (@cmdcolin)
    • #4827 Improve status updating for BedTabixAdapter, Gff3TabixAdapter, VcfTabixAdapter, BigBedAdapter (@cmdcolin)
    • #4825 Handle multiple jobs with the same name (@garrettjstevens)
    • #4826 Calculate most frequent non-ref allele for multi-variant renderer (@cmdcolin)
    • #4824 Aggregate transcript level features in GTF based on "gene_name" field (@cmdcolin)
    • #4810 Ensure embedded users get the latest semver @gmod/vcf for multi-variant fixes (@cmdcolin)
  • app-core, core

:bug: Bug Fix

  • sv-core
    • #4837 Update @gmod/cram for fixed decoding of some CRAM files (@cmdcolin)
  • Other
    • #4808 Fix random palette color generation for multi-variant colors (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.1

Done in 0.69s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.0

3.0.0 (2025-01-29)

:boom: Breaking Change

  • core
  • __mocks__, app-core, core, embedded-core, product-core, sv-core

:rocket: Enhancement

  • Other
  • core, web-core
  • core, product-core
    • #4798 Add more track metadata to UCSC assembly hub loading (@cmdcolin)
  • core
    • #4795 Improved rendering of phased VCF and polyploid VCF in multi-variant view (@cmdcolin)
    • #4792 Allow uploading a sampleTsv file with per-sample metadata for VCF files (@cmdcolin)
    • #4786 Allow opening "synteny tracks" from the default Add track workflow (@cmdcolin)
    • #4785 Allow opening BedGraph et al in the default Add track workflow (@cmdcolin)
    • #4784 Improve UI for choosing query and target assemblies in the "New track" workflow for synteny tracks (@cmdcolin)
    • #4767 Improve load time when multiple tracks use same data file (@cmdcolin)
    • #4750 Add some more lazy loading for smaller bundle size (@cmdcolin)
  • sv-core
    • #4753 Allow launching a single level breakpoint split view focused on the breakends (@cmdcolin)
  • web-core
  • app-core, core
    • #4729 Update cram-js to avoid requesting file size for more CORS compatibility (@cmdcolin)

:bug: Bug Fix

  • Other
    • #4778 Fix GC content calculation consistency across blocks (@cmdcolin)
    • #4773 Fix "Color by CDS" for BED12 features (@cmdcolin)
    • #4771 Fix generating categories for composite tracks in UCSC hubs (@cmdcolin)
    • #4769 Fix facet filter crash (@cmdcolin)
    • #4765 Fix repeat masker track BED interpretation (@cmdcolin)
    • #4764 Fix modifications coverage calculations (@cmdcolin)
    • #4731 Fix naming of subtracks produced by "group by tag" operation (@cmdcolin)
    • #4732 Fix persisting alignments "color by" and "filter by" settings in snapshots/session shares/page reloads (@cmdcolin)
  • core
    • #4776 Fix maximum recursion error in linear synteny view import form (@cmdcolin)
    • #4768 Fix navigation via CIGAR string alignment in synteny view (@cmdcolin)
    • #4766 Fix some bed12 transcripts displaying as bedMethyl features (@cmdcolin)
    • #4727 Fix type confusion where sequence feature details crashes for empty subfeatures (@cmdcolin)
    • #4725 Avoid error on closing draggable dialog and a couple more refactors (@cmdcolin)

:house: Internal

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.18.0

2.18.0 (2024-12-10)

:rocket: Enhancement

  • core, product-core, sv-core
  • Other
  • 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: 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)

:house: Internal

  • __mocks__, app-core, core, embedded-core, product-core, sv-core, text-indexing, web-core
  • Other

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.17.0

2.17.0 (2024-11-18)

:rocket: Enhancement

:bug: Bug Fix

  • Other
  • 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)

:house: Internal

  • core

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.16.1

2.16.1 (2024-11-03)

:rocket: 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: 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

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.16.0

2.16.0 (2024-10-23)

:rocket: Enhancement

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

:bug: 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

:memo: Documentation

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

:house: 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

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.4

2.15.4 (2024-09-20)

:bug: Bug Fix

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.3

Done in 0.57s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.2

2.15.2 (2024-09-18)

:rocket: Enhancement

:bug: Bug Fix

:house: Internal

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

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.1

2.15.1 (2024-09-12)

:rocket: Enhancement

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

:bug: Bug Fix

  • Other
  • core
    • #4553 Fix performance regression since v2.14.0 in assembly loading (@cmdcolin)

:house: Internal

  • core
  • Other

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.15.0

Done in 1.26s.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.14.0

2.14.0 (2024-08-28)

:rocket: 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

:bug: Bug Fix

:house: 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
  • core, product-core, text-indexing

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 2.13.1

2.13.1 (2024-07-31)

:rocket: Enhancement

: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

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

:house: Internal

Committers: 3

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

:memo: Documentation

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

Committers: 1

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

Committers: 2

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

2.11.2 (2024-06-03)

:rocket: Enhancement

:bug: Bug Fix

Committers: 3

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
  • app-core

Committers: 1

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

2.11.0 (2024-04-16)

:rocket: Enhancement

: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

Committers: 3

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

2.10.3 (2024-03-06)

:rocket: Enhancement

: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

Committers: 5

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

Committers: 1

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

2.10.1 (2024-01-09)

:rocket: Enhancement

:bug: Bug Fix

  • Other
  • core
    • #4147 Fix bad svg output in v2.10.0 in cases where feature names have angle brackets (@cmdcolin)

:memo: Documentation

Committers: 2

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
  • 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

:house: Internal

Committers: 2

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

2.9.0 (2023-11-30)

:rocket: Enhancement

  • Other
    • #4070 Add support for single file hubs (@cmdcolin)
    • #4096 Allow searching by gene name using linear synteny view (@cmdcolin)
    • #4068 Allow searching the text-index by gene name from the URL bar (@cmdcolin)
    • #3948 Make the default setting for the dotplot/synteny views use 'Existing tracks' by default (@cmdcolin)
    • #4039 Adds "Favorites" and "Recently used" track categories to the track selector (@carolinebridge-oicr)
    • #4067 Add arc plugin to @jbrowse/react-linear-genome-view core plugins (@cmdcolin)
  • core, product-core
    • #4091 Allow hiding subfeatures in the feature details panel (@cmdcolin)

:bug: Bug Fix

  • core
  • Other
    • #4095 Fix faceted metadata header names colliding with non-metadata header names (@cmdcolin)
    • #4071 Fix Mac auto-updates fetching non-existent zip (@cmdcolin)
    • #4062 Fix duplicate key error in hierarchical track selector from using connections (@cmdcolin)

Committers: 2

yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.8.0

2.8.0 (2023-11-09)

:rocket: Enhancement

  • Other
  • product-core
  • core
    • #4035 Prompt to horizontally flip view when launching linear synteny view on inverted feature (@cmdcolin)
  • app-core

:bug: Bug Fix

  • #4052 Fix browser back button behavior in jbrowse-web (@cmdcolin)
  • #4043 Fix crash in "Open session" widget for sessions that have 'track-less views' (@cmdcolin)

:memo: Documentation

Committers: 2

yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.7.2

2.7.2 (2023-10-27)

:rocket: Enhancement

  • core
  • Other
    • #4020 Allow configuring LGV trackLabels setting via config (@cmdcolin)
    • #3999 Example of using customElement + ShadowDOM for @jbrowse/react-linear-genome-view (@AcaDemIQ)
    • #4015 Create MacOS universal build of jbrowse-desktop to help M1 macs (@cmdcolin)
  • core, product-core

:bug: Bug Fix

:house: Internal

  • core
    • #4005 Refactors and typescript improvements for jbrowse-web loader (@cmdcolin)
  • app-core, core

Committers: 3

yarn run v1.22.19 $ lerna-changelog --silent --next-version 2.7.1

2.7.1 (2023-10-18)

:rocket: Enhancement

  • Other
    • #3986 Allow editing step size and window size of GC content adapter (@cmdcolin)
  • core
    • #3982 Allow rendering semi-circles in the arc renderer + SVG rendering of arcs (@cmdcolin)
  • __mocks__, core
    • #3981 Auto-create HTML links for URLs, and strip HTML tags where they can't be rendered (@cmdcolin)

:bug: Bug Fix

  • Other
    • #3991 Remove some non-functioning options from top level menu in @jbrowse/react-app (@cmdcolin)
    • #3980 Downgrade electron 26->25 to fix screen blanking (@cmdcolin)
  • core
    • #3971 Fix rendering multi-quantitative tracks when blank data is present (@cmdcolin)

Committers: 1

yarn run v1.22.18 $ lerna-changelog --next-version 2.7.0

2.7.0 (2023-10-04)

:rocket: Enhancement

:bug: Bug Fix

  • app-core, core
    • #3959 Remove type any from return value of getContainingView, getSession (@cmdcolin)
  • Other
    • #3946 Fix setting multiple hierarchical defaultCollapsed config options at initialization (@cmdcolin)
    • #3937 Fix dev mode error from LGV overview scalebar (@cmdcolin)
    • #3925 Reduce amount of canvas commands issued to the dotplot renderer (@cmdcolin)
    • #3924 Fix incorrect tick mark label on dotplot axes happening in some cases (@cmdcolin)
    • #3921 Fix hydration warning by only rendering the SvgFeature "selected feature" and "mouseover" client side (@cmdcolin)
    • #3910 Fix feature label offsets in SVG exports with main thread RPC (@cmdcolin)
    • #3905 Fix alignments track infinite loading when applying same "Color by" or "Sort by" setting twice (@cmdcolin)
    • #3904 Fix "Color by"->"Mapping quality" for CRAM files (@cmdcolin)
    • #3902 Fix ability to use plaintext bed in add-track CLI (@cmdcolin)
  • core
    • #3929 Fix mouse getting out of sync while dragging resize handle (@cmdcolin)
    • #3912 Avoid undefined getConf on assembly.configuration safeReference (@cmdcolin)
    • #3887 Add forwardRef to wrapped re-exported lazy components (@garrettjstevens)
    • #3866 Fix calculation of width of "view container title" (@cmdcolin)
    • #3865 Strip alpha from colors for improved SVG export compatibility (@cmdcolin)

:memo: Documentation

  • #3957 Add error handler example for embedded components (@cmdcolin)
  • #3913 Add color scheme for pathogenicity for ClinVar config_demo track (@scottcain)
  • #3881 Improve some of the extension point documentation (@cmdcolin)

:house: Internal

  • app-core, core, embedded-core
  • core
    • #3920 Remove some unused "renameReference" code in static/dynamic blocks (@cmdcolin)
  • Other
  • app-core, core, embedded-core, product-core, web-core

Committers: 4

yarn run v1.22.18 $ lerna-changelog 2.6.3

:rocket: Enhancement

:bug: Bug Fix

  • #3839 Fix bug where multi-quantitative tracks plotted incorrectly for some bigwigs with empty regions (@cmdcolin)
  • #3837 Fix text layout in dotplots with long coordinate strings (@cmdcolin)
  • #3825 Fix SVG export compatibility by removing rgba strings (@cmdcolin)
  • #3814 Fix suspense fallback to track container for lazy loaded display components (@cmdcolin)
  • #3808 Fix track ordering of hierarchical track selector to more closely match the config.json (@cmdcolin)
  • #3806 Fix a bug on the BookmarkWidget mui data grid where labels were not saving (@carolinebridge-oicr)
  • #3804 Fix version missing from about menu in @jbrowse/react-app (@cmdcolin)

:house: Internal

Committers: 3

yarn run v1.22.18 $ lerna-changelog 2.6.2

:rocket: Enhancement

:bug: Bug Fix

  • Other
    • #3798 Fix VCF feature starting at 1-based 1 (@cmdcolin)
    • #3775 Fix stranded RNA-seq rendering and rename option Color by -> "First-of-pair strand" (@cmdcolin)
    • #3758 Adds safety checks on AlignmentsDisplay properties to avoid undefined rendering (@carolinebridge-oicr)
    • #3770 Fix potential issue with display searchFeatureByID being undefined (@cmdcolin)
  • core
  • app-core, core, embedded-core, product-core, text-indexing, web-core
    • #3771 Use inlineSourceMaps for tsc builds and other misc changes (@cmdcolin)

:house: Internal

Committers: 3

yarn run v1.22.18 $ lerna-changelog 2.6.1

:rocket: Enhancement

  • Other
    • #3743 Create mixin for shared code between LinearWiggleDisplay and MultiWiggleLinearDisplay (@cmdcolin)
    • #3711 Allow synteny data adapters to open files larger than 512Mb (@cmdcolin)
    • #3639 Add button to bookmark in jbrowse-web share dialog (@cmdcolin)
    • #3631 Add BEDPE add track workflow, avoid showing "Add track" when disabled (@carolinebridge-oicr)
    • #3700 Render alignment track arcs instantly after bpPerPx change (@cmdcolin)
    • #3695 Reduce re-drawing on alignments track paired read arcs/cloud display types (@cmdcolin)
  • core
    • #3725 Filter tracks that match all view.assemblyNames in multi-assembly track selector modes (@cmdcolin)
    • #3531 Add @jbrowse/react-app embedded component (@cmdcolin)
    • #3653 Evaluate extension point on track config pre-process snapshot (@cmdcolin)
    • #3706 Miscellaneous alignments arc/cloud fixes (@cmdcolin)
    • #3698 Add column resizers to the variant ANN/CSQ panels (@cmdcolin)
  • app-core, product-core, web-core
  • __mocks__
    • #3707 Improved read cloud display for long reads with inversions (@cmdcolin)

:bug: Bug Fix

  • core
    • #3749 Avoid re-prompting a user login when refresh token is processed (@cmdcolin)
    • #3572 Add OAuth and HTTP BasicAuth servers for local testing, fix some OAuth flows (@garrettjstevens)
    • #3708 Add removable-media to jbrowse desktop snap (@cmdcolin)
    • #3687 Take into account ML tag when showing MM tag on alignments, misc refactoring (@cmdcolin)
  • Other
    • #3747 Fix blank lines in GFF crashing text-index (@cmdcolin)
    • #3739 Fix specifying the assemblyNames config slot on add-connection CLI (@cmdcolin)
    • #3631 Add BEDPE add track workflow, avoid showing "Add track" when disabled (@carolinebridge-oicr)
    • #3667 Fix horizontal flip functionality for Hi-C display (@studentshivang)
    • #3703 Fix rendering error in alignments tracks when filtering by tag in CRAM file (@Lilas-w)
    • #3694 Fix ability to filter certain fields in BAM/CRAM files (@cmdcolin)
    • #3691 Fix breakpoint split view alignment connections not pointing at right position in v2.5.0 (@cmdcolin)
    • #3686 Fix jbrowse create/jbrowse upgrade CLI intermittent failures (@cmdcolin)
  • product-core, web-core
    • #3738 Don't throw on UCSC connection containing assemblies not matching connection->assemblyNames config (@cmdcolin)
  • app-core, core, embedded-core
  • app-core

:memo: Documentation

:house: Internal

  • app-core, core, product-core, text-indexing
    • #3740 Bump electron, proxy-agent, fontsource-roboto, etc. and update SnackbarMessage from typed array to object (@cmdcolin)
  • core
    • #3741 Distinguish between SessionWithConnections and SessionWithConnectionEditing (@cmdcolin)
  • Other
  • app-core, core, product-core, web-core
  • product-core
  • app-core, core, embedded-core, product-core, text-indexing
  • core, product-core
    • #3661 Create packages/product-core containing shared code between the various products (@rbuels)

Committers: 6

2.5.0 (2023-05-04)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
  • core
    • #3677 Adjust RefNameAutocomplete width calculation to avoid ellipses (@cmdcolin)
    • #3660 Bump x-data-grid dependency, refactors for BaseFeatureDetails, add GridToolbar (@cmdcolin)
    • #3626 Update to mui x-data-grid 6 (@cmdcolin)

:bug: Bug Fix

  • core
    • #3681 Guard against undefined in CoreGetFeatureDetails (@cmdcolin)
    • #3662 Fix empty feature sequence on top-level gene feature (@cmdcolin)
    • #3666 Fix text boxes being too small in Dialog boxes (@cmdcolin)
    • #3642 Fix error handling of feature detail formatter jexl callbacks (@cmdcolin)
    • #3621 Update plugin rollup polyfill package (@garrettjstevens)
    • #3620 Fix potential crashes where alignment SEQ field may be empty, simplify some display model code (@cmdcolin)
  • Other
    • #3670 Only double-click zoom if not clicking on feature (@cmdcolin)
    • #3652 Fix text being invisible on overview scalebar when cytobands shown (@cmdcolin)
    • #3632 Fix mouse click-and-drag behavior in the alternative "cursor mode" for the dotplot view (@cmdcolin)
    • #3625 Fix UCSC trackhub assembly aliases matching (@andrzejgrzelak)
  • __mocks__, core

:memo: Documentation

  • Other
    • #3676 Refactor circular genome view storybook (@cmdcolin)
    • #3671 Fix website documentation sidebar on browsers with prefers-reduced-motion (@cmdcolin)
    • #3654 Add some docs for configuring defaultSession (@cmdcolin)
  • core

:house: Internal

  • core
    • #3647 Refactoring navToMultiple, navToLocString, and related (@cmdcolin)
    • #3629 Typescript checking for config slot names (@rbuels)
    • #3618 Rename APIs for feature density stats and quantitative stats (@cmdcolin)
    • #3615 Add check for default export to plugin loader (@rbuels)

Committers: 4

2.4.2 (2023-03-27)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #3604 Alignments tags description in feature details on mouseover (@cmdcolin)
  • Other

:bug: Bug Fix

  • Other
    • #3610 Avoid cutting off import form of spreadsheet view, fix overflowed text in table header (@cmdcolin)
    • #3600 Fix using the force load button after a stats timeout (@cmdcolin)
    • #3592 Fix shading on synteny features after mouseout (@cmdcolin)
  • __mocks__, core
    • #3608 Fix subfeatures formatter not being applied to feature detail panel (@cmdcolin)
    • #3607 Avoid "ResizeObserver" loop warning during development (@cmdcolin)
  • core
    • #3593 Fix gene without subfeatures not being displayed in sequence feature details (@cmdcolin)

:house: Internal

  • #3611 Use local data instead of remote data for LGV component test (@cmdcolin)

Committers: 2

2.4.1 (2023-03-14)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication https://www.npmjs.com/package/@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #3534 Improve visibility of SNPs on alignments track (@cmdcolin)
    • #3561 Add scroll zoom, d-pad, and more click+drag options to dotplot (@cmdcolin)
  • Other
    • #3574 Add ability to load all built-in synteny data sources from @jbrowse/cli (@cmdcolin)
    • #3564 Use double-click to zoom in on particular offset in LGV, and make ctrl+scroll also zoom in on particular offset (@cmdcolin)

:bug: Bug Fix

  • #3578 Fix selected synteny feature getting unselected after scroll (@cmdcolin)
  • #3566 Fix use of "show all regions with data" feature in SV inspector with TRA entries (with CHR2 from INFO) (@cmdcolin)
  • #3558 Fix visual effect from using the overview scalebar click and dragging backwards (@cmdcolin)
  • #3556 Fix infinite loading state when no synteny features are visible in synteny view (@cmdcolin)
  • #3551 Fix bad layout on tabix tracks that have Unicode characters (@cmdcolin)
  • #3548 Fix upper case querying of jbrowse 1 text search store (@cmdcolin)
  • #3545 Fix issue where clearing search box on LGV import form turns search box into loading bar (@cmdcolin)

:memo: Documentation

:house: Internal

  • Other
  • __mocks__, core, text-indexing
    • #3557 Add additional lint rules from typescript-eslint and eslint-plugin-unicorn (@cmdcolin)

Committers: 2

2.4.0 (2023-02-24)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication https://www.npmjs.com/package/@jbrowse/plugin-authentication
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
  • core
    • #3513 Add ability to open refNameAliases+cytobands in "Open sequence" start screen on desktop (@cmdcolin)
    • #3512 SVG export of linear synteny view, dotplot, and circular views (@cmdcolin)
    • #3467 Create dark theme and allow user to toggle different themes from preferences dialog (@cmdcolin)

:bug: Bug Fix

:memo: Documentation

Committers: 2

2.3.4 (2023-02-01)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #3494 Use transitionDuration 0 as defaultProp in theme for both popovers and menus (@cmdcolin)
    • #3488 Render HTML in faceted track selector for track data/metadata (@cmdcolin)
    • #3483 Add anchorOrigin/transformOrigin to default menu component (@cmdcolin)
    • #3470 Variant sample grid auto-size columns and resizer (@cmdcolin)
  • Other
    • #3304 Faceted/data grid style track selector (@cmdcolin)
    • #3477 Larger margins to add track workflow to visually clarify next button behavior (@cmdcolin)
    • #3475 Bypass plugins.json download if unneeded during app startup (@cmdcolin)
    • #3458 Improve auto-update of sequence track height when toggling forward/reverse/translation settings (@cmdcolin)

:bug: Bug Fix

  • core
    • #3482 Fix loading external plugins in embedded linear-genome-view demo (@cmdcolin)
  • Other
    • #3457 Fix synteny view not drawing after horizontal flip in v2.3.3 (@cmdcolin)
    • #3459 Booleanize localstorage settings from older versions of LGV to avoid crash (@cmdcolin)

:memo: Documentation

Committers: 1

2.3.3 (2023-01-11)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication https://www.npmjs.com/package/@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gccontent https://www.npmjs.com/package/@jbrowse/plugin-gccontent
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-text-indexing
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #3440 "Show all regions" for dotplot and synteny views and refactor synteny rendering RPC to optimize scrolling (@cmdcolin)

:bug: Bug Fix

  • Other
    • #3451 Fix auto-updates on desktop not working since v2.2.2 (@cmdcolin)
  • core
    • #3428 Add missing dependencies to embedded component package.json's (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 1

2.3.2 (2022-12-20)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gccontent https://www.npmjs.com/package/@jbrowse/plugin-gccontent
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #3422 Auto-adjust height of reference sequence track to current settings (@cmdcolin)
  • Other
    • #3421 Add ability to revcomp sequence in the "Get sequence" dialog (@cmdcolin)
    • #3413 Add a "base" set of tracks and assemblies for the embedded demos (@cmdcolin)

:bug: Bug Fix

  • #3419 Fix rendering base-level alignments on synteny visualizations, especially in inverted regions (@cmdcolin)
  • #3416 Fix rendering alignment arcs on files that need refname renaming and add jitter setting (@cmdcolin)
  • #3415 Fix circular view being rendered as a blank area if tab is opened in the background (@cmdcolin)

Committers: 1

<summary>Packages in this release</summary>

Package Download
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view

2.3.0 (2022-12-15)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication https://www.npmjs.com/package/@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gccontent https://www.npmjs.com/package/@jbrowse/plugin-gccontent
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #3403 Reduce overplotting on dotplot grid lines and other misc improvements (@cmdcolin)
    • #3381 Add method for cache busting requests to the config file in jbrowse-web (@cmdcolin)
    • #3384 Add method to more easily create compact view of alignments (@cmdcolin)
  • core
    • #3391 Allow arc display to connect to "unpaired" positions using RNEXT/PNEXT or SA tag (@cmdcolin)
    • #3387 Small UI tweaks for add track workflow (@cmdcolin)
    • #3358 Create new "arc" display type to show long range connections between paired-end and split-reads (@cmdcolin)
  • text-indexing
    • #3385 Optimize prefix size for text indexing automatically (@cmdcolin)

:bug: Bug Fix

  • Other
    • #3407 Remove trackhub registry plugin from core plugins, moved to plugin store (@cmdcolin)
    • #3406 Fix loading connection tracks from connections that don't specify assemblyNames in config (@cmdcolin)
    • #3390 Fix positioning within large alignments for query->target LGV synteny navigation (@cmdcolin)
    • #3388 Fix search result that matches synonyms that matches multiple locations (@cmdcolin)
  • core
    • #3404 Fix double-render of some synteny features (@cmdcolin)
    • #3401 Remove y-scalebar rendering placeholder values in blank and loading states (@cmdcolin)
    • #3389 Fix issue where snackbar would not show up when same error message is triggered multiple times (@cmdcolin)

:memo: Documentation

  • core
  • Other
    • #3383 Add note to user guide about variant callers that can be used for SV inspector (@cmdcolin)

:house: Internal

  • __mocks__, core, text-indexing
    • #3400 Reduce peerDependency warnings from installing dev environment (@cmdcolin)
  • core

Committers: 1

2.2.2 (2022-12-06)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication https://www.npmjs.com/package/@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gccontent https://www.npmjs.com/package/@jbrowse/plugin-gccontent
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #3350 Retain feature labels in compact display mode for SVG features, and allow turning off keeping feature description without feature label (@cmdcolin)
    • #3357 Allow holding shift key to create rubberband selection on LGV (@cmdcolin)
    • #3363 Create remove-track CLI command (@cmdcolin)
    • #3341 Add BEDPE adapter type (@cmdcolin)
  • core

:bug: Bug Fix

  • Other
    • #3377 Fix rendering and clicking synteny features when using MainThreadRpc (@cmdcolin)
    • #3375 Fix jbrowse upgrade CLI command overwriting config.json with --branch or --nightly options (@cmdcolin)
    • #3370 Fix error with SNPCoverage not rendering MM tag modifications in some cases (@cmdcolin)
    • #3366 Fix ability to use LGV synteny track on inverted alignments (@cmdcolin)
    • #3348 Fix for breakpoint split view and circular view issues with <TRA> type entries in v2.2.1 (@cmdcolin)
  • core
    • #3369 Fix uncaught promise errors and add lint rule for catching these (@cmdcolin)

:memo: Documentation

:house: Internal

  • core
    • #3368 Create base "Dialog" component to standardize dialogs across codebase (@cmdcolin)
  • text-indexing

Committers: 2

2.2.1 (2022-11-21)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication https://www.npmjs.com/package/@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gccontent https://www.npmjs.com/package/@jbrowse/plugin-gccontent
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #3277 Create new "Add track workflow" that allows pasting JSON track configs (@cmdcolin)
    • #3328 Add GC content display type to the reference sequence track (@cmdcolin)
    • #3316 Add LGV typescripting to @jbrowse/react-linear-genome-view (@cmdcolin)
  • core
    • #3298 Add authentication plugin to embedded components (@garrettjstevens)
    • #3329 Add ability to minimize/collapse tracks and views and move views up/down in view stack (@cmdcolin)
    • #3308 Add ability to display synteny track in a normal LGV showing regions of synteny as features (@cmdcolin)
    • #3317 Move ErrorBoundary so that tracks/views that have crashed can be closed more easily (@cmdcolin)

:bug: Bug Fix

  • Other
    • #3342 Fix CRAM mismatches calculation regression in v2.2.0 (@cmdcolin)
    • #3319 Fix pileup "sort by" setting being lost on zoom level change (@cmdcolin)
  • core
    • #3340 Fix linear genome view import form going into infinite loading state changing assemblies with same refnames (@cmdcolin)
    • #3339 Fix force flag for drawing large regions and node-fetch polyfill for node 18 fix in @jbrowse/img (@cmdcolin)

Committers: 2

2.2.0 (2022-11-04)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication https://www.npmjs.com/package/@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
  • core
    • #3299 Add ability to open a synteny track directly from the dotplot/linear synteny view import forms (@cmdcolin)
    • #3287 Lazy-load assemblies on demand instead of all at app startup (@cmdcolin)
    • #3279 Remove unnecessary expanded region query and small refactors (@cmdcolin)

:bug: Bug Fix

  • core
    • #3309 Fix animated "Loading..." message keyframes (@cmdcolin)
    • #3306 Fix the RefNameAutocomplete displaying a stale value for chromosome names (@cmdcolin)
    • #3302 Improve rubberband zooming across elided regions (@cmdcolin)
  • Other
    • #3293 Fix CRAM plotting for data files that encode insertions in uncommon way (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 3

2.1.7 (2022-10-20)

<summary>Packages in this release</summary>

Package Download
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view

:bug: Bug Fix

  • #3282 Fix for embedded build with webpack 4 failing with v2.1.6 (@cmdcolin)

Committers: 1

2.1.6 (2022-10-19)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #3272 Disable resolution of Derives_from fields in GFF3 parsing, fixes TAIR gff (@cmdcolin)
    • #3254 Use tick labels that correspond to the overview's larger zoom level (@cmdcolin)
  • core
    • #3230 Add ability to customize About dialog with callbacks and optionally hide links to data (@cmdcolin)
    • #3275 Add help dialog for feature sequence panel (@cmdcolin)
    • #3250 Handle alternate line endings (@garrettjstevens)
    • #3252 Fix gene sequence fetching in embedded, and allow fetching genomic sequence for other feature types (@cmdcolin)
  • core, text-indexing

:bug: Bug Fix

:memo: Documentation

:house: Internal

Committers: 3

2.1.5 (2022-10-03)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #3200 Use Alert component for track messages (@garrettjstevens)
    • #3229 Allow user to select local assembly to add tracks to for trackhub registry (@cmdcolin)
    • #3220 Improve error reporting on SV inspector/spreadsheet view on import form (@cmdcolin)
    • #3198 Improve error reporting on jbrowse-web start screen when user attempts to open a broken recent session (@carolinebridge-oicr)
  • core
    • #3223 Allow adding session tracks to embedded react component along with disableAddTracks option if unwanted (@cmdcolin)
    • #3227 Add infrastructure for creating linear-genome-view sub-classes (@carolinebridge-oicr)
    • #3215 Add error boundary on view, track, and drawer widget (@cmdcolin)
    • #3216 Add ability to set number of bp to fetch up/down stream/inside intron in feature details (@cmdcolin)

:bug: Bug Fix

  • Other
    • #3241 Fix local session failing to load copying between tabs in some cases (@cmdcolin)
    • #3234 Fix circular embedded view failing to load in v2.1.3 and v2.1.4 (@cmdcolin)
    • #3233 Fix legend being cutoff on multiwiggle tracks with wide window (@cmdcolin)
    • #3217 Fix loading tracks from connection using assembly alias (@cmdcolin)
    • #3214 Fix trackhub registry failing to load in 2.x.y versions of jbrowse (@cmdcolin)
    • #3204 Fix authentication configuration on jbrowse-desktop (@cmdcolin)
  • core

:memo: Documentation

:house: Internal

Committers: 3

2.1.4 (2022-09-16)

<summary>Packages in this release</summary>

Package Download
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view

:bug: Bug Fix

  • #3191 Fix the UMD build of the react embedded components (@cmdcolin)

Committers: 1

2.1.3 (2022-09-15)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #3188 Add 'Open saved session' button to start screen on desktop (@cmdcolin)
    • #3187 Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table (@cmdcolin)
    • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
    • #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
    • #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
    • #3162 Add about dialog with version number for embedded components (@cmdcolin)
    • #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
    • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
    • #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
    • #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
    • #3162 Add about dialog with version number for embedded components (@cmdcolin)
    • #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
  • core

:bug: Bug Fix

  • core
    • #3168 Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form (@cmdcolin)
    • #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
    • #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
  • Other

:memo: Documentation

:house: Internal

Committers: 3

<summary>Packages in this release</summary>

Package Download
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

2.1.1 (2022-08-25)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • Other
    • #3157 Support the "name" field on multi-wiggle adapter subadapters instead of source (@cmdcolin)
    • #3154 Use the union of all the subadapter refNames for the MultiWiggleAdapter getRefNames (@cmdcolin)
    • #3156 Fix for mouseover/mouse click on wiggle/multi-wiggle causing errors in embedded mode (@cmdcolin)
    • #3151 Fix ability to click and drag overview scale bar dragging right to left (@cmdcolin)
    • #3133 Update the ref name box when assembly is changed in LGV import form (@garrettjstevens)
    • #3131 Use "code" instead of "key" for undo/redo keyboard event, fixes shift+ctrl+z redo (@garrettjstevens)
    • #3119 Use es2015 setting for commonjs builds of packages to fix @jbrowse/img (@cmdcolin)
    • #3142 Fix unicode arrow icon not rendering with some fonts in configuration editor (@garrettjstevens)
  • core
    • #3120 Fix menu items for changing display type from track menu (@cmdcolin)

Committers: 2

2.1.0 (2022-07-28)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #3111 Create undo manager in jbrowse-web and jbrowse-desktop (@cmdcolin)
    • #3115 Add warning when dotplot renders outside of it's boundaries, and create click-and-drag panning of dotplot view (@cmdcolin)
    • #3102 Allow creating alternative "add track workflows" from within the "Add track" widget (@cmdcolin)
    • #3043 Create MultiWiggle track type, adapter, and renderers (@cmdcolin)
  • Other
    • #3113 Improve SVG performance by avoiding re-render when feature is clicked (@cmdcolin)
    • #3110 Remove TSDX from plugin development tools (@garrettjstevens)
    • #3106 Add "emphasis" mode for no fill/scatterplot mode in XYPlot type renderings (@cmdcolin)

:bug: Bug Fix

  • Other
    • #3109 Better support for developing plugins from within yarn 2+ workspaces (include __virtual folder in build) (@garrettjstevens)
  • core

:memo: Documentation

Committers: 2

2.0.1 (2022-07-13)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • Other
    • #3088 Fix labels being cut-off in SVG features by rendering feature labels on main thread (@cmdcolin)
    • #3085 Fix zoom to behavior being inaccurate with many displayed regions visible (@cmdcolin)
    • #3082 Fix negative strand CIGAR renderings on linear synteny view (@cmdcolin)
    • #3077 Fix crash opening multiple synteny track selectors launched from dotplot view (@cmdcolin)
  • core
    • #3086 Fix pxToBp and bpToPx calculations when there are many displayed regions (@cmdcolin)

Committers: 2

2.0.0 (2022-07-07)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #3001 Draw SNPs in modifications/methylation views (@cmdcolin)
    • #3068 Allow HTML in feature tooltips, remove react-simple-code-editor (@cmdcolin)
    • #3065 Allow changing between xyplot,line,density for linear wiggle tracks and other small fixes (@cmdcolin)
  • text-indexing
    • #3058 Improve bundle size and code splitting on embedded builds (v2) (@cmdcolin)
  • __mocks__, core, text-indexing
    • #2949 Upgrade to MUI v5, mobx-state-tree v5, mobx-react v6, mobx-react v7 (@cmdcolin)

:bug: Bug Fix

  • Other
  • core
    • #3064 Fix opening link in new tab by default in feature details (@cmdcolin)
    • #3053 Avoid displaying [object Object] on deeply nested data in base feature details (@cmdcolin)

:house: Internal

Committers: 2

1.7.11 (2022-06-22)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #3044 Remove node-canvas from @jbrowse/core dependencies (@cmdcolin)
    • #3041 Fix ability to search and load data files using lower case refName aliases (@cmdcolin)
  • Other

:bug: Bug Fix

  • #3049 Fix ability to use callbacks for the linear arc renderer (@cmdcolin)

:memo: Documentation

:house: Internal

  • core

Committers: 1

1.7.10 (2022-06-13)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #3025 Add dotplot session spec (@cmdcolin)
    • #2975 Add simplified URL format for loading synteny views (@cmdcolin)
    • #3023 Add error handling in case of invalid OAuth2 configuration used. (@andrzejgrzelak)
    • #3020 Allow choosing trackId when using text-index with --file with --fileId (@cmdcolin)
    • #3016 Allow whitespace separated refname,start,end type locstring (@cmdcolin)
    • #3006 Add string array configuration slot UI improvements (@cmdcolin)
    • #2998 Avoid rendering offscreen contents in pileup renderer (@cmdcolin)
    • #3000 Add reference base and correct percentage calculations to tooltip on SNPCoverage display (@cmdcolin)
  • core
    • #2981 Add simplified URL format for loading spreadsheet and SV inspector (@cmdcolin)
    • #2990 Use shortened megabases (M) display when zoomed out, and option to hide the "open track selector" button (@carolinebridge-oicr)
    • #3003 Add ability to run field formatters on the feature details panel (@cmdcolin)
    • #3017 Add button to copy track config in About track dialog (@cmdcolin)
    • #2999 Generate clickable links to track data in about track dialog (@cmdcolin)
  • __mocks__, core
    • #3005 Use cascading menu helper library for track menu to avoid menu going offscreen (@cmdcolin)

:bug: Bug Fix

Committers: 3

1.7.9 (2022-06-02)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #2991 Use canvas2svg for SVG export, fixes non-rasterized usage of bezier, arcs, and more (@cmdcolin)
    • #2483 Add setting to color by query score per alignment for dotplot, support HTML in config slot descriptions (@cmdcolin)
    • #2983 Set target=_blank by default in user HTML links (@cmdcolin)
  • Other

:bug: Bug Fix

  • core
  • Other
    • #2977 Respect --indexFile option when adding VCF and BED tracks (@heavywatal)
    • #2974 Fix track indexing being ignored after first add track widget usage (@teresam856)

:house: Internal

Committers: 4

1.7.8 (2022-05-20)

<summary>Packages in this release</summary>

Package Download
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • #2969 Fix link on yeast synteny demo and fix CIGAR rendering on dotplot (@cmdcolin)
  • #2964 Fix crash displaying modifications called on softclipped regions of reads (@cmdcolin)
  • #2965 Fix filter functionality on pileup tracks (@cmdcolin)
  • #2953 Fix "Open" button on LGV ImportForm (@cmdcolin)
  • #2952 Fix read vs ref not finding primary alignment on certain CRAM files (@cmdcolin)
  • #2951 Fix viewing soft/hardclip indicator in some regions (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 2

1.7.7 (2022-05-04)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-linear-comparative-view
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:bug: Bug Fix

:house: Internal

  • core
    • #2944 Avoid stalling on undefined assemblyName during ref name renaming (@cmdcolin)

Committers: 1

1.7.6 (2022-04-26)

<summary>Packages in this release</summary>

Package Download
@jbrowse/desktop

:bug: Bug Fix

  • #2939 Fix loading CRAM, TwoBit, and other modules that use @gmod/binary-parser on jbrowse desktop (@cmdcolin)

Committers: 1

1.7.5 (2022-04-26)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-jobs-management
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #2885 Reduce serialization overhead on alignments tracks and access feature details asynchronously (@cmdcolin)
  • Other
    • #2935 Use the name "Read Sequence" for the read vs ref view (@cmdcolin)
    • #2916 Add vite setup to our embedded component demos (@cmdcolin)
    • #2927 Optimize gtf by only parsing lazily per-refName (@cmdcolin)
    • #2928 Add vanillajs/script tag loading embedded components demos (@cmdcolin)
  • core, text-indexing

:bug: Bug Fix

  • #2863 Render gene with CDS subfeatures properly (@cmdcolin)
  • #2934 Bump @gmod/trix to fix prefix size calculation and searching first word in index (@cmdcolin)

Committers: 3

1.7.4 (2022-04-19)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:bug: Bug Fix

Committers: 2

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

<summary>Packages in this release</summary>

Package Download
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view

1.7.1 (2022-04-15)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:bug: Bug Fix

  • core
    • #2917 Create tsconfig.build.json to add types to plugins/embedded components (@cmdcolin)
  • Other

:memo: Documentation

  • #2903 Add download link for jbrowse web on downloads page (@cmdcolin)

Committers: 1

1.7.0 (2022-04-14)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #2909 Add --prefixSize flag to @jbrowse/cli text-index (@cmdcolin)
    • #2887 Optimize filtering on alignments tracks (@cmdcolin)
    • #2879 Multi-level synteny rubberband (@cmdcolin)
    • #2874 Optimizations for rendering long syntenic alignments e.g. CHM13 vs GRCh38 (@cmdcolin)
    • #2872 Better connection between paired-end alignments in breakpoint split view and optimizations (@cmdcolin)
  • core
    • #2902 Standardize heights of widgets in LGV import form (@cmdcolin)
    • #2781 Add floating labels to SVG features (@cmdcolin)
    • #2875 Make assembly selector remember your last selected assembly (@cmdcolin)
    • #2860 Avoid performing many peekTransferables to optimize RPC serialization (@rbuels)

:bug: Bug Fix

  • Other
    • #2908 Fix AboutDialog under vite for embedded components (@cmdcolin)
    • #2900 Fix the 'Open assembly' menu item in jbrowse desktop (@cmdcolin)
    • #2882 Add padding at the bottom of the configuration editor to help color editing popup being cutoff (@cmdcolin)
    • #2877 Fix strand on arrows in horizontally flipped mode (@cmdcolin)
  • core
    • #2891 Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components (@cmdcolin)

:memo: Documentation

:house: Internal

  • core
    • #2904 Use a user-supplied fetchCJS callback to import CJS plugins (@cmdcolin)
    • #2891 Use a user-supplied fetchESM callback to import ESM plugins to fix 'Critical dependency...' errors from embedded components (@cmdcolin)
    • #2857 Refactor and improve types of OffscreenCanvas shim and ponyfill (@rbuels)
  • __mocks__, core

Committers: 3

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

1.6.8 (2022-03-25)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • Other
    • #2852 Fix misaligned features under breakpoint split view (@cmdcolin)
    • #2844 Fix layout of small features without labels for SvgFeatureRenderer (@cmdcolin)
    • #2839 Fix the drawing of SNP height when the SNPCoverage track is using log scale (@cmdcolin)
    • #2825 Fix tracklabels positioning not updating in UI after user selection (@cmdcolin)
  • core

Committers: 3

1.6.7 (2022-03-16)

<summary>Packages in this release</summary>

Package Download
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

Committers: 2

1.6.6 (2022-03-15)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-tools https://www.npmjs.com/package/@jbrowse/development-tools
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #2796 Add collapsible accordion sections in configuration editor (@cmdcolin)
    • #2791 Add new coloring options for dotplot and ability to "rectangularize" dotplot view (@cmdcolin)
    • #2741 Allow ability to enter a space-separated locstring to open a list of regions (@cmdcolin)
    • #2725 Refactor InternetAccounts, add standard getFetcher (@garrettjstevens)
    • #2787 Display the total bp viewed in the header of the dotplot view (@cmdcolin)
    • #2767 Wiggle and SNPCoverage look and feel improvements (@cmdcolin)
    • #2746 Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view (@cmdcolin)
  • Other
    • #2799 Exit process after rendering to speed up jb2export (@cmdcolin)
    • #2793 Add abortcontroller polyfill to jbrowse-img to allow it to run under node 14 (@cmdcolin)
    • #2761 Add a --clean argument to jbrowse upgrade to clean up old files (@cmdcolin)
    • #2760 Make a configurable refNameColumn in RefNameAliasAdapter (@cmdcolin)

:bug: Bug Fix

  • core
  • Other
    • #2797 Fix crash plotting methylation in sparse regions (@cmdcolin)
    • #2782 Fix display of cytobands when horizontally flipped (@cmdcolin)
    • #2678 Preserve double border line when using trackLabel offset and use smaller gap between snpcoverage and reads (@cmdcolin)
    • #2774 Fix overwriting broken symlink with --force in add-track CLI (@cmdcolin)
    • #2773 Fix using global stats autoscale on wiggle tracks (@cmdcolin)
    • #2766 Add a check for empty content blocks to fix rare empty stats estimation (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 2

1.6.5 (2022-02-18)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • Other
    • #2758 Use VariantTrack for plaintext VCF type (@cmdcolin)
    • #2738 Add better catch for XS and TS tag detection from CRAM (@cmdcolin)
    • #2733 Use sparse array for alignments coverage to fix bug viewing large sparse regions (@cmdcolin)
    • #2734 Use node fetch instead of follow-redirects in cli (@cmdcolin)
    • #2726 Handle .bgz file extension for text-index (@cmdcolin)
    • #2727 Add engines 16 to @jbrowse/img (@cmdcolin)
    • #2723 Make jbrowse desktop more robust to errors when reading recent sessions file (@cmdcolin)
    • #2715 Change --target to --root for jbrowse CLI admin-server (@cmdcolin)
  • core
    • #2757 Fix type confusion with stats estimation causing BAM files to fail byte size calculation (@cmdcolin)
    • #2750 Add bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in alignments track in webkit and firefox (@cmdcolin)
    • #2719 Avoid uninitialized state during stats estimation (@cmdcolin)
    • #2707 Fix ability to use authenticated assembly files (@garrettjstevens)
    • #2695 Fix disabled state on the linear genome view track labels dropdown menu (@cmdcolin)

:memo: Documentation

  • #2716 Update to node12 requirement for @jbrowse/cli (@cmdcolin)
  • #2605 Developer guide reorganization and create new API document (@cmdcolin)

:house: Internal

Committers: 3

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

<summary>Packages in this release</summary>

Package Download
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

1.6.0 (2022-01-28)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

:memo: Documentation

  • #2663 Add documentation for URL params and session spec (@cmdcolin)
  • #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)

:house: Internal

  • core
    • #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
    • #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
  • Other
    • #2657 Fix hot reload using yarn resolution on react-error-overlay (@cmdcolin)

Committers: 3

1.6.0 (2022-01-28)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

:memo: Documentation

  • #2663 Add documentation for URL params and session spec (@cmdcolin)
  • #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)

:house: Internal

  • core
    • #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
    • #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
  • Other
    • #2657 Fix hot reload using yarn resolution on react-error-overlay (@cmdcolin)

Committers: 3

1.6.0 (2022-01-28)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

:memo: Documentation

  • #2663 Add documentation for URL params and session spec (@cmdcolin)
  • #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)

:house: Internal

  • core
    • #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
    • #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
  • Other
    • #2657 Fix hot reload using yarn resolution on react-error-overlay (@cmdcolin)

Committers: 3

1.5.9 (2022-01-13)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:bug: Bug Fix

Committers: 1

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

1.5.7 (2022-01-13)

<summary>Packages in this release</summary>

Package Download
@jbrowse/plugin-dotplot-view
@jbrowse/desktop
@jbrowse/web

:rocket: Enhancement

Committers: 1

1.5.6 (2022-01-12)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #2629 Add ability to get parent feature in jexl syntax with either parent(feature) or get(feature,'parent') (@cmdcolin)

Committers: 2

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

1.5.4 (2022-01-07)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-tools https://www.npmjs.com/package/@jbrowse/development-tools
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

:house: Internal

Committers: 3

1.5.3 (2021-12-21)

<summary>Packages in this release</summary>

Package Download
@jbrowse/development-tools https://www.npmjs.com/package/@jbrowse/development-tools

:bug: Bug Fix

Committers: 1

1.5.2 (2021-12-20)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-tools https://www.npmjs.com/package/@jbrowse/development-tools
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #2579 Add help text and help dialog for the RefNameAutocomplete (@cmdcolin)
    • #2553 Add sashimi-style arcs for RNA-seq type skips on SNPCoverage display (@cmdcolin)
    • #2552 Change border on non-cytoband OverviewScaleBar visible region back to blue and cytoband OverviewScaleBar to a little lighter fill (@cmdcolin)
    • #2509 Implement prop interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer (@hextraza)
    • #2485 Only use one button, "Go", in text search ambiguous results dialog (@cmdcolin)
    • #2501 Add a tooltip to desktop session path so you can see the full path if it's cut off (@garrettjstevens)
  • core
  • core, development-tools
    • #2487 Add support for additional types of plugin formats (commonjs, esm) to allow access to node modules on jbrowse desktop (@garrettjstevens)

:bug: Bug Fix

  • Other
    • #2594 Fix infinite loop bug while searching certain strings and handle multi-word searches better (@cmdcolin)
    • #2589 Fix occasional failures observed from running text-index command (@cmdcolin)
    • #2583 Fix for alignments track base modifications display regarding skipped bases on Mm tag (@cmdcolin)
    • #2556 Fix ability to access BigWig tracks on http basic auth for some cases (@cmdcolin)
    • #2577 Fix ability to use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, GTF support to add-track CLI (@cmdcolin)
    • #2521 Fix ability to search for tracks with parentheses in tracklist (@cmdcolin)
    • #2512 Fix [object Window] issue in alignment read vs reference dialog (@cmdcolin)
    • #2499 Add missing dependency to CLI (@garrettjstevens)
  • core
    • #2585 Fix ability to use "Color by methylation" on files that require refname renaming (@cmdcolin)
    • #2517 Remove aborting on adapter loading process to fix some tracks getting stuck in infinite loading state (@cmdcolin)
    • #2564 Start looking for parents with parent, not self in findParentThat (@garrettjstevens)
    • #2563 Restore ability to load plugins from relative URL (@garrettjstevens)
    • #2533 Fix drawer widget minimized button being unclickable when overlapping with a view (@cmdcolin)

:memo: Documentation

:house: Internal

  • core
    • #2597 Fix flaky tests related to auth and canvas image snapshots (@cmdcolin)
    • #2504 Spreadsheet change jbrequire to es6 imports (@cmdcolin)

Committers: 6

1.5.1 (2021-11-04)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-gtf https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #2488 Improve usability of the search result autocomplete when typing in via keyboard (@cmdcolin)
    • #2267 Add cytoband to overview scale bar in LGV (@cmdcolin)
    • #2447 Drawer widget tooltips and use position: fixed on fab (@cmdcolin)
    • #2299 Add new pluggable element type and properties to adapter type for registering adapter association with 'add track' workflow (@carolinebridge-oicr)
  • Other

:bug: Bug Fix

  • Other
    • #2494 Add polyfill for text-index compatibility with node 10 (@cmdcolin)
    • #2492 Fix ability to open breakpoint split view from a BEDPE row in SV inspector (@cmdcolin)
    • #2480 Fix refName renaming on VcfAdapter for files that don't have ##contig lines (@cmdcolin)
    • #2469 Fix embedded crash when opening dialogs (@garrettjstevens)
    • #2451 Fix issue with intermittent text-index failures and improve speed (@cmdcolin)
    • #2439 Fix adding plugins on desktop (@cmdcolin)
    • #2426 Fix CLI create/upgrade failing to find the latest release (@cmdcolin)
  • core
    • #2457 Fix linear synteny view import form failure (@cmdcolin)
    • #2444 Fix crash when chromSizesLocation not specified when loading TwoBitAdapter in GUI (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 4

1.5.0 (2021-10-18)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trix https://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/img https://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #2413 Bundle size savings (@cmdcolin)
    • #2390 Support plain text (non-tabix'ed) GFF files with new Gff3Adapter (@teresam856)
    • #2384 Allow docking the drawer on the left side of the screen (@cmdcolin)
    • #2387 Add bulk delete of sessions on jbrowse-desktop (@cmdcolin)
    • #2279 Add ability to access authenticated resources using pluggable internet accounts framework (@peterkxie)
  • Other
    • #2388 Create "quickstart list" on jbrowse-desktop which users can add to (@cmdcolin)
    • #2385 Ensure all dependencies are properly specified in package.json files using eslint-plugin-import (@cmdcolin)
    • #2373 Add auto update functionality for jbrowse-desktop (@cmdcolin)
    • #2369 Add tooltip with track description to track selector (@garrettjstevens)
    • #2258 Update admin-server to accept value from ?config= so that multiple configs could be edited (@cmdcolin)
    • #2321 Add show descriptions toggle box to most feature tracks (@cmdcolin)

:bug: Bug Fix

  • Other
    • #2355 Allow prefix and exact matches jb1 text search (@cmdcolin)
    • #2348 Fix ability to use JB1 backcompat text search adapter (@teresam856)
    • #2322 Fix install plugin workflow and error handling on desktop, update to electron 15 (@cmdcolin)
    • #2329 Fix bugs preventing embedded circular genome view from rendering in some circumstances (@garrettjstevens)
  • core
    • #2352 Better keyboard navigations on text search autocomplete component (@cmdcolin)
    • #2332 Fix ability to use LocalFile on nodejs-based apps e.g. @jbrowse/img (@cmdcolin)

:memo: Documentation

:house: Internal

  • Other
  • core
    • #2379 Bump typescript to 4.4.3 (@cmdcolin)
    • #2363 Add some typescripting of some MST models and components (@cmdcolin)
    • #2351 Use main "module" field instead of "browser" from dependency package json files electron builds (@cmdcolin)
    • #2323 Remove session related menu items from jbrowse-desktop (@cmdcolin)

Committers: 6

1.4.4 (2021-09-14)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trix
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #2287 Use react-popper to reduce tooltip lag on pages with many elements (@cmdcolin)
    • #2294 Don't rely on SVTYPE=BND for breakend split view options and thicker mouseover chords on circular views (@cmdcolin)
    • #2272 Auto adjust box RefNameAutocomplete width based on refName length (@cmdcolin)
    • #2243 Import bookmarks functionality for grid bookmark widget (@cmdcolin)
  • core
    • #2247 New jbrowse-desktop start screen design (@cmdcolin)
    • #2254 Better error reporting from web worker and chrom sizes adapter errors (@cmdcolin)
    • #1881 Add new text searching functionality to core, with jbrowse text-index CLI command to generate trix index (@teresam856)

:bug: Bug Fix

  • core
    • #2320 Fix issue where add track widget doesn't infer adapters on second usage (@cmdcolin)
    • #2250 Prevent the ToggleButton for the FileSelector toggling to local file when only URL should be available (@cmdcolin)
  • Other
    • #2309 Fix mouseover selection appearing across unrelated blocks (@cmdcolin)
    • #2283 Fix ability for the variant detail panel to create breakpoint split view for <TRA> elements (@cmdcolin)
    • #2268 Fix autocomplete height on small displays (@cmdcolin)

:memo: Documentation

  • #2300 Release announcement draft v1.4.0 (@teresam856)
  • #2310 Add cancer demos to the demos page on website (@cmdcolin)
  • #2253 Add note about legacy-peer-deps to embedded component readme (@cmdcolin)
  • #2262 Add more MDX documentation pages to @jbrowse/react-linear-genome-view storybooks (@cmdcolin)

:house: Internal

Committers: 3

1.4.3

Failed NPM upload, partial release

1.4.2

Failed NPM upload, partial release

1.4.1

Broken releases missing some packages

1.4.0

Broken releases missing some packages

1.3.5 (2021-08-23)

<summary>Packages in this release</summary>

Package Download
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view

1.3.4 (2021-08-23)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-grid-bookmark https://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-circular-genome-view https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #2163 Add new embeddable React Circular Genome View (@garrettjstevens)
    • #2229 Use extendPluggableElement for context menu items (@garrettjstevens)
    • #2233 Add optional chromSizes config slot to TwoBitAdapter to speed up loading of TwoBit files with many refseqs (@cmdcolin)
    • #2199 Make the BED parser not interpret general tab delimited data as BED12 (@cmdcolin)
    • #2241 Restore previous window location when re-opening on desktop (@garrettjstevens)
    • #2203 Add a helpful message if there is a 404 on config.json error (@cmdcolin)
    • #2204 Hide reads with unmapped flag by default in alignments tracks (@cmdcolin)
    • #2198 Add better inversion visualization to read vs reference visualizations (@cmdcolin)
    • #2154 Add UMD build of react-linear-genome-view for plain-js use (@garrettjstevens)
  • core

:bug: Bug Fix

:memo: Documentation

:house: Internal

  • core
    • #2057 Use idMaker for dataAdapterCache key for faster FromConfigAdapter performance (@cmdcolin)
    • #2231 Export offscreenCanvasUtils (@cmdcolin)
    • #2226 Use superRenderProps and superTrackMenuItems for better simulated inheritance model (@cmdcolin)
    • #1874 Add aborting to CoreGetFeatures rpcManager call (@cmdcolin)
  • Other

Committers: 4

1.3.3 (2021-08-02)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • Other
    • #2159 Stop local storage quota-exceeded errors preventing the app from starting (@cmdcolin)
    • #2161 Remove outline from clicking on SVG chord tracks (@cmdcolin)
    • #2157 Fix rendering of negative strand alignment modifications/methylation (@cmdcolin)
    • #2131 Fix mouseovers/click handlers after "force load" button pressed (@cmdcolin)
    • #2128 Fix using the "Color by modifications" setting on files that need ref renaming (@cmdcolin)
    • #2115 Fix bug where sometimes plugin could not be removed from UI (@garrettjstevens)
    • #2119 Fix loading indicator on the reference sequence selector getting stuck (@cmdcolin)
  • core
    • #2101 Fix behavior of the end-of-list indicator in refNameAutocomplete to always display as a disabled item (@teresam856)

:house: Internal

Committers: 3

1.3.2 (2021-07-07)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/desktop
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • #2109 Make sure to wait for assembly to load before downloading canonical refnames in SV inspector (@cmdcolin)
  • #2111 Fix "Can't resolve '@jbrowse/plugin-legacy-jbrowse'" in @jbrowse/react-linear-genome-view (@garrettjstevens)

Committers: 2

1.3.1 (2021-07-06)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse https://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • Other
    • #2097 Improve speed for laying out features for embedded/mainthreadrpc scenarios (@cmdcolin)
    • #2096 Fix issue with page reload after editing session title (@cmdcolin)
    • #2074 Fix support for opening local files in spreadsheet/SV inspector (@cmdcolin)
    • #2061 Fix issue with using --force error when no track was previously loaded (@cmdcolin)
    • #2024 Flip drawing of negative strand PAF features in linear synteny and dotplot views (@cmdcolin)
    • #2023 Fix infinite loop in adding some plugins on desktop (@cmdcolin)
    • #2019 Fix session import to use blob map for opening local files (@cmdcolin)
  • core
    • #2071 Add indicator to the end of ref name dropdown to suggest user to type the searchbox for more (@teresam856)
    • #2056 Fix infinite recursion in FromConfigAdaptor by avoiding mutating the passed in data when using SimpleFeature (@cmdcolin)
    • #2018 Fix 3'UTR in sequence detail panels when no UTRs are in gff (@cmdcolin)

:house: Internal

Committers: 5

1.3.0 (2021-05-24)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-tools https://www.npmjs.com/package/@jbrowse/development-tools
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
    • #2001 Make tracks added using the add track widget a session track if not in adminMode (@cmdcolin)
    • #1980 Add popup confirmation dialog for unknown session plugins, and use plugins.json as a whitelist (@cmdcolin)
    • #1977 Upgrade @material-ui/data-grid (@cmdcolin)
  • core
    • #1982 Allow manually specifying adapter type if filename does not match expected pattern (@cmdcolin)
    • #1975 Allow local files on the users computer to be opened as tracks in jbrowse-web (@cmdcolin)
    • #1865 Show modified bases using MM and MP/ML tags in BAM/CRAM (@cmdcolin)
    • #1984 Better feature details when there are short arrays of json supplied as feature data (@cmdcolin)
    • #1931 Create in app graphical plugin store (@elliothershberg)

:bug: Bug Fix

  • core
    • #1985 Avoid error calculating UTR on features that have no exon subfeatures (@cmdcolin)
    • #1954 Add more environments to configSchema create calls to fix ability to use custom jexl commands with main thread rendering (@cmdcolin)
    • #1963 Fix ability to use DialogComponent (used for svg export, pileup sort, etc) on embedded components (@cmdcolin)
    • #1945 Fix hic not being able to render due to incorrect lazy loading (@cmdcolin)
  • Other

:memo: Documentation

  • #2002 Add @jbrowse/img to homepage (@cmdcolin)
  • #2007 Update docs for modifications/methylation coloring, plugin store, and the sequence panel in feature details (@cmdcolin)
  • #1976 reorganize the demo page to emphasize the cancer sv demo more (@rbuels)
  • #1952 Add demo for 1000 genomes extended trio dataset to website (@cmdcolin)
  • #1862 Add example for using a build-time included plugin to storybook (@cmdcolin)

:house: Internal

  • Other
    • #2003 Make SNPCoverage independently generate the modifications tag-color mapping (@cmdcolin)
  • core, development-tools

Committers: 4

1.2.0 (2021-05-03)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #1125 Export SVG (@cmdcolin)
    • #1867 Virtualized tree for tracklist to support having thousands of tracks (@cmdcolin)
    • #1660 Allow connections to have multiple assemblies (@garrettjstevens)
    • #1864 Add Material UI's DataGrid to re-exports (@garrettjstevens)
    • #1875 Make drawer widget titles stay visible when scrolling inside the widget (@cmdcolin)
    • #1877 Add ability to copy the text produced by the feature details sequence panel to MS Word/Google Docs and preserve styling (@cmdcolin)
    • #1854 Make "About track" dialog available from tracklist and for non-LGV tracks (@cmdcolin)
    • #1853 Add mouseovers in feature details that show field descriptions for VCF fields (@cmdcolin)
  • Other
    • #1892 Create new JB2 plugin store (@elliothershberg)
    • #1901 Make using --out for add-assembly create output directory if it does not exist and fix outputting to symlink (@cmdcolin)
    • #1850 Add true breakend ALT strings to the feature details panel (@cmdcolin)
    • #1878 Add --delete to set-default-session, fix --session (@garrettjstevens)
    • #1861 Change Alignments track "Fade mismatches by quality" setting to a separate config param and made it less strict (@cmdcolin)

:bug: Bug Fix

  • core
    • #1924 Fix import of BED and navToLocString from spreadsheet views (@cmdcolin)
    • #1918 Fix issue with some falsy values being hidden in feature details (@cmdcolin)
    • #1911 Fix breakpoint split view visualizations for files that need ref renaming (e.g. chr1 vs 1) (@cmdcolin)
    • #1904 Fix issue with synteny polygons displaying slightly offset (@cmdcolin)
    • #1884 Fix rIC ponyfill for use on Safari (@cmdcolin)
  • Other
    • #1912 Fix reloading of local sessions when using React.StrictMode (@cmdcolin)
    • #1900 Make clicking away from autocomplete popup on track container work (@cmdcolin)
    • #1878 Add --delete to set-default-session, fix --session (@garrettjstevens)
    • #1871 Fix crash on dotplot/linear synteny import form and when closing linear synteny track (@cmdcolin)
    • #1860 Fix alignments read filter jexl syntax (@cmdcolin)

:memo: Documentation

  • #1914 Use MDX to add proper image captions in web and pdf documentation (@cmdcolin)
  • #1855 Add download page in website header and new super-quick-start guide (@cmdcolin)

:house: Internal

Committers: 4

1.1.0 (2021-03-29)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #1846 Improve copy+paste in the data grids for feature details (@cmdcolin)
    • #1814 Add ability to get promoter sequence and intron sequence for genes from the feature details panel (@cmdcolin)
    • #1816 Remove some animation effects (@cmdcolin)
    • #1778 Adds dropdown to show drawer widget stack (@teresam856)
    • #1685 Change callbacks language from JavaScript to Jexl (@peterkxie)
  • Other
    • #1831 Add dialog for launching breakpoint split view from variant feature details (@cmdcolin)
    • #1803 Transcript and gene glyphs can now display implied UTRs, active by default (@cmdcolin)
    • #1808 Add another heuristic for returning gene features from BigBed (@cmdcolin)
    • #1774 Add warning dialog in LGV before returning to import form to prevent accidentally losing the current view (@cmdcolin)

:bug: Bug Fix

:memo: Documentation

:house: Internal

Committers: 6

1.0.4 (2021-03-08)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/protein-widget
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #1758 Add ability to get stitched together CDS, protein, and cDNA sequences in feature details (@cmdcolin)
    • #1721 Manually adjust feature height and spacing on alignments track (@cmdcolin)
    • #1728 Add list of loaded plugins to the "About widget" (@rbuels)
    • #1711 Add plugin top-level configuration (@teresam856)
    • #1699 Add sequence track for both read and reference genome in the "Linear read vs ref" comparison (@cmdcolin)
    • #1701 Add clickable navigation links to supplementary alignments/paired ends locations and BND/TRA endpoints in detail widgets (@cmdcolin)
    • #1601 Add ability to color by per-base quality in alignment tracks (@cmdcolin)
    • #1640 Move stats calculation to BaseFeatureAdapter (@cmdcolin)
    • #1588 Add "Get sequence" action to LGV rubber-band (@teresam856)
  • Other
    • #1743 Add color picker and choice of summary score style for wiggle track (@cmdcolin)
    • #1763 Add a "CSS reset" to jbrowse-react-linear-genome-view to prevent parent styles from outside the component leaking in (@cmdcolin)
    • #1756 Split alignments track menu items into "Pileup" and "SNPCoverage" submenus (@cmdcolin)
    • #1742 Add ability to display crosshatches on the wiggle line/xyplot renderer (@cmdcolin)
    • #1736 Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs (@cmdcolin)
    • #1394 Add new menu items for show/hide feature labels, set max height, and set compact display mode (@cmdcolin)
    • #1720 Standardize phred qual scaling between BAM and CRAM and add option to make mismatches render in a lighter color when quality is low (@cmdcolin)
    • #1704 Add "Show all regions in assembly" to import form and make import form show entire region when refName selected (@cmdcolin)
    • #1687 Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events (@cmdcolin)
    • #1695 Improve zoomed-out display of quantitative displays tracks when bicolor pivot is active (@cmdcolin)
    • #1680 Add on click functionality to quantitative track features (@teresam856)
    • #1630 Get column names from BED tabix files and other utils for external jbrowse-plugin-gwas support (@cmdcolin)
    • #1709 Improve sorting and filtering in variant detail widget (@cmdcolin)
    • #1688 Bold insertion indicator for large insertions on pileup track (@cmdcolin)
    • #1669 Allow plain json encoding of the session in the URL (@cmdcolin)
    • #1642 Enable locstring navigation from LGV import form (@teresam856)
    • #1655 Add GFF3Tabix and BEDTabix inference to JB1 connection (@garrettjstevens)
    • #1643 Add an offset that allows all wiggle y-scalebar labels to be visible (@cmdcolin)
    • #1632 Displays warnings when receiving a session with custom callbacks (@peterkxie)
    • #1615 Increase pileup maxHeight (@cmdcolin)
    • #1624 GCContent adapter (@cmdcolin)
    • #1614 Add insertion and clip indicators to SNPCoverage views (part of Alignments tracks) (@cmdcolin)
    • #1610 Display error message from dynamodb session sharing error (@cmdcolin)

:bug: Bug Fix

  • Other
    • #1777 Quick fix for block error (@cmdcolin)
    • #1748 External plugins load after confirming config warning (@peterkxie)
    • #1750 Fix pileup sorting when using string tag (@cmdcolin)
    • #1747 Fix the position of the popup menu after rubberband select when there is a margin on the component e.g. in embedded (@cmdcolin)
    • #1736 Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs (@cmdcolin)
    • #1731 Fix alignment track ability to remember the height of the SNPCoverage subtrack on refresh (@cmdcolin)
    • #1719 Fix for navigation past end of chromosome (@cmdcolin)
    • #1698 Fix rendering read vs ref comparisons with CIGAR strings that use = sign matches (@cmdcolin)
    • #1697 Fix softclipping configuration setting causing bases to be missed (@cmdcolin)
    • #1689 Disable copy/delete menu items for reference sequence track (@teresam856)
    • #1682 Fix parsing of BED and BEDPE files with comment header for spreadsheet view (@cmdcolin)
    • #1679 Fix issue with using launching the add track widget on views that are not displaying any regions (@teresam856)
    • #1642 Enable locstring navigation from LGV import form (@teresam856)
    • #1626 Bug Fix: specify assembly in locstring (@teresam856)
    • #1619 Fix overview scale polygon not appearing properly in some cases (@cmdcolin)
  • core

:memo: Documentation

:house: Internal

Committers: 7

1.0.3 (2021-01-11)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-tools https://www.npmjs.com/package/@jbrowse/development-tools
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/protein-widget
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • Other
  • core
    • #1531 Add track menu options for autoscale, log scale, histogram fill, setting min/max score, and zoom level/resolution for wiggle/snpcoverage tracks (@cmdcolin)
    • #1473 Color, filter, and sort options for the alignments (@cmdcolin)
    • #1576 Add location string to tooltip for wiggle and SNPCoverage tracks (@cmdcolin)
    • #1529 Display subfeatures in feature details widget (@cmdcolin)
  • core, development-tools

:bug: Bug Fix

  • Other
    • #1608 Take into account offsetX of the rubberband on scalebar zooming (@cmdcolin)
    • #1597 Fix crash when there are undefined references in the state tree e.g. when a track is deleted but still referred to by a session (@peterkxie)
    • #1598 Disable 'copy to clipboard' while share url being generated (@peterkxie)
    • #1589 Fix the display of trackhub registry results (@cmdcolin)
    • #1573 Update hic-straw to fix error for hic files with many scaffolds (@cmdcolin)
    • #1563 Remove softclip and hardclip from being counted as SNPs in the SNPCoverage (@cmdcolin)
    • #1559 Avoid errors from breakpoint split view related to getBoundingClientRect on null track (@cmdcolin)
    • #1540 Fix memory leak when side scrolling LGV blocks (@cmdcolin)
    • #1534 Fix breakpoint split view showing too many connections for paired end ends (@cmdcolin)
    • #1524 Move loading flag for spreadsheet import wizard to volatile to avoid it persisting across refresh (@cmdcolin)
    • #1521 Add missing dep to react-linear-genome-view (@garrettjstevens)
  • core
    • #1587 Fix positioning of scalebar tooltips, overview scalebar plotting, and refName label positioning when displaying many regions (@cmdcolin)
    • #1547 Fix analytics crashing when using plugins (@cmdcolin)

:memo: Documentation

  • #1594 Add GFF3 example to quickstart (@cmdcolin)
  • #1581 Add some features that are missing from jbrowse 2 to the feature comparison table (@cmdcolin)
  • #1558 Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo (@cmdcolin)
  • #1537 Add CONTRIBUTING.md with tips for getting started with codebase (@cmdcolin)

:house: Internal

Committers: 6

v1.0.2 (2020-12-02)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-tools https://www.npmjs.com/package/@jbrowse/development-tools
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view https://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/protein-widget
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

  • core
    • #1513 Add a custom scrollbar that overrides the auto-hiding behavior of scrollbars on OSX (@elliothershberg)

:bug: Bug Fix

  • Other
    • #1514 react-linear-genome-view bug fixes (@garrettjstevens)
    • #1517 Fix the use of filtering display on desktop (@cmdcolin)
    • #1512 Fix setting maxDisplayedBpPerPx for pileup display, helps prevent too large an area from being rendered (@cmdcolin)
    • #1442 Change track selector togglebutton to normal button (@cmdcolin)
    • #1506 Fix horizontally flipped translation frames position (@cmdcolin)
    • #1501 Fix CLI to allow jbrowse create to download newer monorepo tag format (@cmdcolin)
  • core

Committers: 3

v1.0.1 (2020-11-25)

<summary>Packages in this release</summary>

Package Download
@jbrowse/core https://www.npmjs.com/package/@jbrowse/core
@jbrowse/development-tools https://www.npmjs.com/package/@jbrowse/development-tools
@jbrowse/plugin-alignments https://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bed https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-view
@jbrowse/plugin-config https://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-management https://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-filtering
@jbrowse/plugin-gff3 https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequence https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svg https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-variants https://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wiggle https://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/cli https://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/protein-widget
@jbrowse/react-linear-genome-view https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

:rocket: Enhancement

:bug: Bug Fix

  • core
    • #1491 Fix ability to add a PAF synteny track with add-track (@cmdcolin)
    • #1470 Avoid rendering the literal string 'null' in the feature details (@cmdcolin)
  • Other
    • #1489 Fix long read vs ref CIGAR rendering for horizontally flipped synteny view (@cmdcolin)
    • #1460 Add support for more bigBed subtypes and fallback for unsupported types (@peterkxie)
    • #1472 Wait on assemblies that are being tracked by the assemblyManager only (@cmdcolin)
    • #1466 Avoid rendering the display and renderer settings in the about this track dialog (@cmdcolin)
    • #1461 Fix usage of jbrowse-cli on node 10.9 related to fs.promises (@cmdcolin)
    • #1452 Bug: search box disappears from LGV header on smaller widths (@teresam856)
    • #1432 Make global variables window.JBrowseSession and window.JBrowseRootModel available in jbrowse-web (@teresam856)
    • #1431 Fix connection tracks not showing up in track selector (@garrettjstevens)
    • #1428 Fix the listVersions behavior of the jbrowse-cli returning duplicate entries (@cmdcolin)
    • #1422 Fix crash from empty ALT field in VCF (@cmdcolin)
    • #1413 Fix ability to add CRAM tracks using the web based add-track GUI (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 5