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:

• Schedule 1-on-1 appointment

Pre-requisites

• git
• nodejs (node 18 or greater)
• yarn

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/

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
  • #5049 Add react compiler (@cmdcolin)
• app-core, core
  • #5044 Allow plugins to register entries onto the root configuration (@cmdcolin)

:bug: Bug Fix

• Other
  • #5062 Fix useSWR usage from plugins (@cmdcolin)
  • #5053 Fix @jbrowse/img using a no-op css import (@cmdcolin)
  • #5051 Fix race condition with text search using useEffect cleanup (@cmdcolin)
• core
  • #5058 Improve speed of navigation for fragmented assemblies (@cmdcolin)

:memo: Documentation

• #5047 Reduce the embedded website tutorial (@cmdcolin)

:house: Internal

• Other
  • #5057 Reduce S3 uploads per-branch (@cmdcolin)
  • #5054 Add ability to make commits to update docs only and avoid running CI (@cmdcolin)
• core
  • #5061 Modularize some integration tests for launching views (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.94s.

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
  • #5029 Fix data grid re-exports (@cmdcolin)

:house: Internal

• core
  • #5039 Add titleNode prop to @jbrowse/core/ui/Dialog (@cmdcolin)
• Other
  • #5036 Remove the async keyword from BaseLinearDisplayModel (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.78s.

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

• #5005 Updated screenshots in gallery (@cmdcolin)
• #5001 Improve website docs with grammarly suggestions (@cmdcolin)
• #4982 Add example of disabling side-scroll/zoom in embedded lgv (@cmdcolin)
• #4977 Fix addToExtensionPoint example in docs (@garrettjstevens)

:house: Internal

• core, product-core
  • #5011 Remove some unused functions on the session model (@cmdcolin)
• core
  • #5003 Fix typescript on renderToAbstractCanvas (@cmdcolin)
  • #4994 Refactor some ReExport code (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.68s.

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

3.3.0 (2025-04-18)

:rocket: Enhancement

• core
  • #4956 Add simplified display of REF/ALT to help with long strings produced by e.g. Cactus VCF (@cmdcolin)
  • #4954 Add genotype frequency table to variant feature details (@cmdcolin)
  • #4952 Add 'genotype' column to the Variant sample grid (@cmdcolin)
  • #4944 Show ALT allele description on multi-variant mouseover (@cmdcolin)
  • #4922 Add Multi-variant SV display (@cmdcolin)
• Other
  • #4950 Add ability to use jexl filters on multi-sample variant displays (@cmdcolin)
  • #4934 Add alpha-transparency to help show overlapping SVs in the Multi-sample variant display (@cmdcolin)
  • #4931 Show target zoom level in tooltip on slider (@cmdcolin)
  • #4930 Upload last release build to https://jbrowse.org/code/jb2/latest (@cmdcolin)
• app-core, core, embedded-core, product-core, sv-core, web-core
  • #4933 Upgrade to MUI v6 -> MUI v7 (@cmdcolin)

:bug: Bug Fix

• Other
  • #4929 Fix broken bigbed features when there is gene level aggregation (@cmdcolin)
• core
  • #4923 Fix dark stock theme showing bad colors (@cmdcolin)

: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
  • #4925 Update docs with phased VCF tutorial (@cmdcolin)

:house: Internal

• core
  • #4926 Skip running hydration for server side rendering (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.41s.

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

• Colin Diesh (@cmdcolin) Done in 1.00s.

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
  • #4237 Add ability for views to pin elements, such as headers and tracks (@garrettjstevens)

:bug: Bug Fix

• core
  • #4867 Fix web worker usage of lollipop renderer (@cmdcolin)
• Other
  • #4883 Bump @gmod/bam for CSI index fix (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.07s.

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

3.0.5 (2025-03-04)

:bug: Bug Fix

• #4864 Bump trix to fix bug fetching some search results (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.24s.

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

3.0.4 (2025-03-01)

:rocket: Enhancement

• Other
  • #4856 Add status callback while parsing .delta (MUMmer), .chain (liftover) and PIF files (@cmdcolin)
  • #4855 Handle case insensitive UTR (@cmdcolin)
  • #4853 Split VCF adapter (@cmdcolin)
  • #4848 Allow clicking feature even if there is a slight mouse drag (@cmdcolin)
  • #4847 Add mouseover color and resize handle to variant matrix view (@cmdcolin)
  • #4846 Increase color clarity in the multi-variant viewer (@cmdcolin)
• 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

• core
  • #4843 Remove usage of some deprecated APIs (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.14s.

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
  • #4819 Use assembly "displayName" field on View titles (@cmdcolin)

: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

• #4838 2024 year in review blog post (@cmdcolin)

:house: Internal

• #4835 Move plugin devtools to it's own repo (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.91s.

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
  • #4716 Update to generic-filehandle2 (@cmdcolin)
• __mocks__, app-core, core, embedded-core, product-core, sv-core
  • #4702 Update to react 19 (@cmdcolin)

:rocket: Enhancement

• Other
  • #4789 Allow user to edit region size as 'Custom zoom' (@cmdcolin)
  • #4796 Make any bigType track open as BigBedAdapter in ucsc connections (@cmdcolin)
  • #4788 Allow supplying a tsv of sample metadata with VCF for multi-variant views (@cmdcolin)
  • #4782 Add track filetype guesser for BedGraph (@cmdcolin)
  • #4774 Restore concept of linking synteny views (@cmdcolin)
  • #4770 Add turbo-zoom buttons (@cmdcolin)
  • #4756 Improved mouseover on alignment squiggles in breakpoint split view (@cmdcolin)
  • #4736 Bulk delete session tracks (@cmdcolin)
  • #4733 Add option to 'Hide small indels (less than 10bp)' (@cmdcolin)
• core, web-core
  • #4799 Add genotype to multi-variant mouseover (@cmdcolin)
• 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
  • #4745 Add ability to load a ?hubURL= from URL bar (@cmdcolin)
• 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

• #4791 Fix storybook vcf failing to load in dev server (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Kim Rutherford (@kimrutherford) Done in 2.19s.

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

:bug: 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
  • #4680 Add eslint-plugin-import for sort ordering (@cmdcolin)
• Other
  • #4675 Add fix for potential hydration mismatch errors (@cmdcolin)

Committers: 1

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

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

2.17.0 (2024-11-18)

:rocket: Enhancement

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

:bug: Bug Fix

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

:house: Internal

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

Committers: 2

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

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

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

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
  • #4430 Multi-level synteny rendering (@cmdcolin)

: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
  • #4600 Fix check for "hasSubSubfeatures" in svg feature rendering (@cmdcolin)
  • #4590 Fix opening .jbrowse files on desktop (@cmdcolin)

: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
  • #4606 Remove react-error-boundary (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.02s.

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

2.15.4 (2024-09-20)

:bug: Bug Fix

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

Committers: 1

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

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

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

:bug: Bug Fix

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

:house: Internal

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

Committers: 1

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

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
  • #4556 Add dropdown menu from bookmark label clicks (@cmdcolin)
• core
  • #4554 Fix the ability to sort menu items by priority for CascadingMenu (@cmdcolin)

:bug: Bug Fix

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

:house: Internal

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

Committers: 1

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

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
  • #4519 Add "Group by" method for alignments tracks (@cmdcolin)

:bug: Bug Fix

• #4535 Fix crash after navToLocString in some cases (@cmdcolin)

: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
  • #4510 Add biome lint fixes (@cmdcolin)
• core, product-core, text-indexing
  • #4508 Use @mui/x-charts-vendor for d3 upgrade (@cmdcolin)

Committers: 2

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

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

2.13.1 (2024-07-31)

:rocket: Enhancement

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

:bug: Bug Fix

• #4501 Fix opening track selector in linear synteny view causing crash in v2.13.0 (@cmdcolin)
• #4495 Fix log scale for some types of signal tracks (@cmdcolin)

Committers: 1

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

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

2.13.0 (2024-07-25)

:rocket: Enhancement

• #4494 Add assembly name to scalebar in synteny views (@cmdcolin)
• #4480 Changes default height for SVG rendering to maxHeight to fix blank track effect on slow CPU (@carolinebridge)
• #4478 Add ability to use CSI indexes in @jbrowse/img (@cmdcolin)

:bug: Bug Fix

• core
  • #4483 Fix configuration settings for track sorting in the track selector (@cmdcolin)
• Other
  • #4476 Fix config editor crash in vite usage of embedded components in dev mode (@cmdcolin)
  • #4473 Fix 'Show no tracks active button' checkbox not working (@cmdcolin)

:memo: Documentation

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

:house: Internal

• core
  • #4493 Remove prop-types from re-exports (@cmdcolin)
  • #4492 Change abortable-promise-cache to @gmod/abortable-promise-cache (@cmdcolin)
• Other
  • #4488 Fix autogen docs build (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge)
• Colin Diesh (@cmdcolin)
• @Maarten-vd-Sande Done in 1.66s.

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

2.12.3 (2024-06-27)

:rocket: Enhancement

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

:bug: Bug Fix

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

:memo: Documentation

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

Committers: 1

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

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

Done in 0.74s.

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

Done in 0.81s.

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

2.12.0 (2024-06-20)

:rocket: Enhancement

• Other
  • #4459 Allow using keyboard shortcut for devtools in production desktop builds (@cmdcolin)
  • #4455 Add slot.type to configuration editor elements (@cmdcolin)
  • #4427 Add ctrl+wheel scroll to zoom both top and bottom of synteny view (@cmdcolin)
  • #4425 Add ability to dismiss dotplot warnings (@cmdcolin)
  • #4422 Make initial linear synteny view import form submit show all regions by default (@cmdcolin)
• core
  • #4456 Add aggregation to BigBedAdapter to group bigGenePred transcripts (@cmdcolin)
  • #4448 Adds genomic coordinates back into the sequence panel accounting for strand direction (@carolinebridge)
  • #4423 Speed up large displayedRegions sets by converting MST array of Region[] into a types.frozen<IRegion[]> (@cmdcolin)
  • #4399 Allow viewing coordinates in sequence feature display panel (@cmdcolin)
• app-core
  • #4443 Allow drawer widget to be "popped out" into a dialog box (@cmdcolin)
• core, product-core
  • #3992 Add ability to get refNames for a track in the "About track" panel (@cmdcolin)

:bug: Bug Fix

• Other
  • #4458 Fix sandbox error on AppImage startup on certain linux systems (@cmdcolin)
  • #4441 Fix sorting data grid on multi-wiggle 'Edit colors/arrangement' dialog (@cmdcolin)
  • #4439 Fix blank lines in multi-wiggle add track workflow causing crash (@cmdcolin)
  • #4438 Fix cursor:pointer style on an alignments feature detail clickable link (@cmdcolin)
  • #4436 Fix "Open synteny view at this position" when file contains CIGAR X/= operators (@cmdcolin)
  • #4426 Fix side scroll in linear synteny view causing the browser "back" action (@cmdcolin)
  • #4417 Fix error message shown on chromosomes with missing data for plaintext GFF3 (@cmdcolin)
• core
  • #4442 Fix unstable dialog width in "About track" dialog for multi-quantitative tracks (@cmdcolin)

:house: Internal

• #4445 Update oclif/test and oclif/core (@cmdcolin)
• #4440 Use ref instead of deprecated findDOMNode for draggable dialog (@cmdcolin)
• #4429 Remove normalize-wheel library (@cmdcolin)
• #4400 Remove node-polyfill-webpack-plugin (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge)
• Colin Diesh (@cmdcolin) Done in 1.71s.

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

2.11.2 (2024-06-03)

:rocket: Enhancement

• Other
  • #4406 Allow loading plaintext GFF3 files larger than 512Mb (@cmdcolin)
  • #4398 Adds a context menu option to zoom to a feature (@carolinebridge)
• core
  • #4405 Include a raw version of function names in error message stack traces (@cmdcolin)
  • #4393 Allow users to configure filters and set them at runtime via a editable dialog (@cmdcolin)
  • #4395 Remove x-data-grid resize bar workaround (@cmdcolin)
  • #4389 Improve return type of intersection2 (@garrettjstevens)

:bug: Bug Fix

• #4407 Fix custom theme being applied in renderings in desktop (@cmdcolin)
• #4402 Fix for rendering of softclipping when there are insertions in the sequence (@cmdcolin)
• #4385 Fix ability to choose line plot bigwig coloring (@cmdcolin)
• #4386 Fix ability to add custom frame colors (@garrettjstevens)

Committers: 3

• Caroline Bridge (@carolinebridge)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.23s.

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

2.11.1 (2024-05-11)

:rocket: Enhancement

• core
  • #4354 Allow capitalizing CDS sequences and lowercasing introns in sequence feature panel (@cmdcolin)
• Other
  • #4351 Store and retrieve user track selector settings in local storage (@cmdcolin)

:bug: Bug Fix

• core
  • #4381 Replace all rgba(...) color strings with rgb(...) in SVG exports to fix usage in illustrator/inkscape (@cmdcolin)
  • #4364 Fix tooltips creating a scrollbar when overflowing off the screen in Chrome (@cmdcolin)
• Other
  • #4366 Fix for regex sequence search on reverse strand features (@cmdcolin)
  • #4362 Auto-detect file format better when importing BED or TSV bookmarks (@cmdcolin)
  • #4357 Fix bookmark showing up on wrong assembly/crashing (@cmdcolin)
  • #4353 Remove snap package (@cmdcolin)
• app-core
  • #4350 Fix Fab positioning on @jbrowse/react-app (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.13s.

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

2.11.0 (2024-04-16)

:rocket: Enhancement

• core
  • #4341 Improve error dialog stack trace display and fix usage on https sites (@cmdcolin)
  • #4340 Change email on error message dialog (@cmdcolin)
  • #4288 Create GCContentTrack type (@cmdcolin)
  • #4312 Update @mui/x-data-grid 6->7 (@cmdcolin)
  • #4280 Add JSON.parse utility to the "jexl function library" (@cmdcolin)
  • #4276 Add retry method to share link dialog in case of error (@cmdcolin)
  • #4266 Add bookmark highlight to overview scale bar (@carolinebridge-oicr)
• Other
  • #4335 Add ability to create multiple highlights on the linear genome view (@carolinebridge-oicr)
  • #4287 Fix snap package and also add deb package (@cmdcolin)
  • #4034 Subtler minicontrols focus (@cmdcolin)
• app-core, product-core
  • #4337 Allow moving tracks and views up/down/to top/to bottom, and better click and drag track re-ordering (@cmdcolin)
• core, product-core
  • #4336 Add new Hi-C color schemes with log scale mode (@cmdcolin)
• core, web-core
  • #4284 Allow getting stack trace error dialog from session.notify errors (@cmdcolin)

:bug: Bug Fix

• Other
  • #4318 Use node-fetch-native to fix warning from JBrowse CLI on node 21+ (@cmdcolin)
  • #4319 Fix Hi-C rendering for some high resolution files (@cmdcolin)
  • #4314 Fix loading of BED12 data from a plaintext BED with column headers (@cmdcolin)
  • #4293 Fix alignment curves showing up in inkscape for breakpoint svg (@cmdcolin)
  • #4287 Fix snap package and also add deb package (@cmdcolin)
  • #4277 Fix usage of --assemblyNames in jbrowse add-connection (@cmdcolin)
  • #4275 Fixes bug on URL highlight param in which refName aliases were not working (@carolinebridge-oicr)
• text-indexing
  • #4269 Avoid crash on badly encoded GFF attributes (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.85s.

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

2.10.3 (2024-03-06)

:rocket: Enhancement

• Other
  • #4257 Smaller sequence track size (@cmdcolin)
  • #4256 Update deps including electron 28->29 (@cmdcolin)
  • #4234 Adds URL query param for highlight on LGV (@carolinebridge-oicr)
• core, product-core
  • #4255 Allow getting stack trace from track errors (@cmdcolin)

:bug: Bug Fix

• #4254 Throw if no sequenceAdapter supplied to CramAdapter (@cmdcolin)
• #4250 Fix the viewport calculations for when URL params includes &tracklist=true (@cmdcolin)
• #4232 Fix for missing INFO.STRANDS tag for TRA features in breakpoint split view (@cmdcolin)
• #4224 Fix parsing of BAM and CRAM refNames that contain a colon (@cmdcolin)

:memo: Documentation

• #4240 Small fixes to embedding tutorial docs (@kwentine)
• #4223 Add FAQ section about faceted track selector (@Maarten-vd-Sande)

Committers: 5

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Quentin Agren (@kwentine)
• @Maarten-vd-Sande Done in 1.56s.

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

2.10.2 (2024-02-19)

:rocket: Enhancement

• Other
  • #4219 Add ability to render only snpcoverage in jbrowse-img (@cmdcolin)
  • #4196 Allow adding &tracklist=true to URL bar to open the track selector, &nav=false to hide linear genome view header (@cmdcolin)
• core
  • #4215 Launch breakpoint split view directly from alignments feature details (@cmdcolin)
  • #4184 Add ability to get stack trace for error messages in the UI (@cmdcolin)

:bug: Bug Fix

• Other
  • #4220 Fix hydration error from translocation features in plaintext VCF adapter (@cmdcolin)
  • #4217 Fix breakpoint split view SVG export occasionally having wrong clipping (@cmdcolin)
  • #4213 Fix issue with tagFilter * in alignments track (@cmdcolin)
  • #4208 Fix @jbrowse/img under node environment (@cmdcolin)
  • #4146 Remove --tracks and --view options from set-default-session CLI (@cmdcolin)
• core
  • #4190 Remove text selection on sequence track with user-select: none (@cmdcolin)
• core, product-core
  • #4177 Fix session tracks being displayed in the tracklist on @jbrowse/react-linear-genome-view (@cmdcolin)

:memo: Documentation

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

Committers: 1

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

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

2.10.1 (2024-01-09)

:rocket: Enhancement

• core
  • #4155 Remove react-svg-tooltip library (@cmdcolin)
• Other
  • #4152 Add directional feet to breakends in linear arc display (@cmdcolin)
  • #4143 Add webpack build for @jbrowse/react-app (@cmdcolin)

:bug: Bug Fix

• Other
  • #4158 Fix subfeature refNames on BED and BEDTabix parsers (@cmdcolin)
  • #4154 Fix metadata facet filters being blank (@cmdcolin)
• core
  • #4147 Fix bad svg output in v2.10.0 in cases where feature names have angle brackets (@cmdcolin)

:memo: Documentation

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

Committers: 2

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

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

2.10.0 (2023-12-15)

:rocket: Enhancement

• core
  • #4138 Speed up large FromConfigAdapter usages with alternative adapter id calculation (@cmdcolin)
  • #4114 Improve pluginManager.jexl typescript definition (@cmdcolin)
• Other
  • #4135 Split "recently used tracks" local storage keys by view assemblies (@cmdcolin)
  • #4003 Adds the ability to highlight regions using the bookmarks widget (@carolinebridge-oicr)
  • #4123 Remove session.notify after using the Add track workflow (@cmdcolin)
  • #3859 Add new pairwise indexed PAF adapter format with CLI creation workflow (@cmdcolin)
  • #4109 Allow right clicking synteny features (@cmdcolin)
  • #4110 Scroll both panels of the linear synteny view when side scrolling the middle panel (@cmdcolin)
  • #4108 Convert to floating-ui for tooltips for small speedup (@cmdcolin)
  • #4107 Refactors and bundle size improvements (@cmdcolin)
• app-core, core
  • #4134 Add ability to click and drag synteny area of synteny view to side scroll (@cmdcolin)

:bug: Bug Fix

• Other
  • #4137 Fix dotplot axis ticks going out of bounds (@cmdcolin)
• core
  • #4136 Fix "Export SVG" feature in next 14 (@cmdcolin)
  • #4125 Fix internet accounts not being shown in file selector after page refresh and hide HTTP basic internet accounts (@cmdcolin)
• app-core, embedded-core
  • #4121 Fix view menu checkboxes not responding in some cases (@cmdcolin)

:memo: Documentation

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

:house: Internal

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

Committers: 2

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

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

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
  • #4094 Refactor faceted track selector to use more MST state (@cmdcolin)
  • #4086 Fix issue where --load inPlace and --force can sometimes remove file unexpectedly (@cmdcolin)
  • #4059 Fix missing icons on some cascading menus (@carolinebridge-oicr)
• 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

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin) Done in 1.41s.

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

2.8.0 (2023-11-09)

:rocket: Enhancement

• Other
  • #4045 Create multi-region arc display type for variant tracks (@cmdcolin)
  • #4050 Allow specifying alternative config.json path via global variable (@cmdcolin)
  • #4046 Show last autosave on jbrowse-web start screen (@cmdcolin)
  • #4044 Speed up "multi-region" navigation in search box (@cmdcolin)
  • #4032 Add jbrowse sort-gff subcommand (@cmdcolin)
• product-core
  • #4040 Strip baseUri in 'About track' copy config (@cmdcolin)
• core
  • #4035 Prompt to horizontally flip view when launching linear synteny view on inverted feature (@cmdcolin)
• app-core
  • #4024 Add right-handed arrow to view title to emphasize the focused view (@carolinebridge-oicr)

: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

• #4027 Add office hours and community meetings (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin) Done in 2.23s.

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

2.7.2 (2023-10-27)

:rocket: Enhancement

• core
  • #3923 Proposal: Add "extendWorker" extension point (@garrettjstevens)
• 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
  • #4013 Create concept of global hovered state (@cmdcolin)

:bug: Bug Fix

• #4016 Fix mouseover tooltip getting stuck after region select popup in dotplot (@cmdcolin)
• #4007 Update cram-js for bzip2 fix (@cmdcolin)

:house: Internal

• core
  • #4005 Refactors and typescript improvements for jbrowse-web loader (@cmdcolin)
• app-core, core
  • #3994 Refactors for app-core view container (@cmdcolin)

Committers: 3

• Alexey Mukhin (@AcaDemIQ)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.56s.

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

• Colin Diesh (@cmdcolin) Done in 1.65s.

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

2.7.0 (2023-10-04)

:rocket: Enhancement

• Other
  • #3956 Make faceted track selector facet filters responsive to adjacent filter selections (@cmdcolin)
  • #3953 Report JSON parse error when failing to load JSON file on desktop (@cmdcolin)
  • #3951 Add jobs widget to jbrowse-web (@carolinebridge-oicr)
  • #3900 Make bookmarks persistent across sessions with local storage (@carolinebridge-oicr)
  • #3896 Upgrade oclif to v3 to avoid deprecation warnings (@garrettjstevens)
  • #3907 Change the config.json missing screen to an "It worked!" message (@cmdcolin)
  • #3901 Use shortened VCF feature description for some types of insertions and deletions (@cmdcolin)
  • #3840 Adds custom filtering option to alignments tracks (@carolinebridge-oicr)
  • #3832 Adds keyboard shortcuts for panning and zooming on a focused view (@carolinebridge-oicr)
• core
  • #3954 Add column resizing for jbrowse-desktop start screen recent sessions panel (@cmdcolin)
  • #3938 Adds code improvements to GridBookmarkWidget (@carolinebridge-oicr)
  • #3914 Swap out NPM color library for colord library (@cmdcolin)
• app-core, core, embedded-core
  • #3931 Add eslint-plugin-fast-refresh (@cmdcolin)
• app-core
  • #3916 Use theme.secondary.main instead of theme.secondary.light on focusedView (@cmdcolin)
• app-core, core, embedded-core, product-core, text-indexing, web-core
  • #3502 Update to react v18, mobx-react v9 (@cmdcolin)
  • #3885 Eject react-script config from jbrowse-web and jbrowse-desktop (@cmdcolin)
• app-core, core, web-core
  • #3831 Adds session model reference to view in focus (@carolinebridge-oicr)

: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
  • #3931 Add eslint-plugin-fast-refresh (@cmdcolin)
• core
  • #3920 Remove some unused "renameReference" code in static/dynamic blocks (@cmdcolin)
• Other
  • #3882 Minor refactors and typescripting improvements (@cmdcolin)
• app-core, core, embedded-core, product-core, web-core
  • #3855 Replace shortid with vendored nanoid (@cmdcolin)

Committers: 4

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Scott Cain (@scottcain) Done in 2.80s.

yarn run v1.22.18 $ lerna-changelog 2.6.3

:rocket: Enhancement

• Other
  • #3830 Refactors LGV synteny and pileup with shared mixins (@carolinebridge-oicr)
  • #3811 Add ability to show/hide all tracks in category (@cmdcolin)
• app-core
  • #3810 Add sorting and collapsing options to the hierarchical track selector (@cmdcolin)
  • #3827 Add check for document.activeElement == INPUT before undo/redo (@cmdcolin)

: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

• #3818 Miscellaneous plugin store code refactoring (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Robert Buels (@rbuels) Done in 1.50s.

yarn run v1.22.18 $ lerna-changelog 2.6.2

:rocket: Enhancement

• #3796 Allow workers to load CJS plugins (@garrettjstevens)
• #3783 Add ability for track selector button in synteny view to select individual views (@cmdcolin)
• #3452 Use notarytool for macOS desktop signing (@cmdcolin)
• #3766 Add nextjs circular genome view demo (@cmdcolin)

: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
  • #3784 Fix synteny rubberband tooltips when views are exactly the same (@cmdcolin)
  • #3782 Fix crash on color picker component using debounce on color property (@carolinebridge-oicr)
  • #3767 Check session tracks for text search adapters (@garrettjstevens)
• app-core, core, embedded-core, product-core, text-indexing, web-core
  • #3771 Use inlineSourceMaps for tsc builds and other misc changes (@cmdcolin)

:house: Internal

• Other
  • #3794 Move embedded demos to individual repos (@cmdcolin)
• core, product-core
  • #3786 Centralize rpcWorker in product-core (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens) Done in 1.55s.

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
  • #3531 Add @jbrowse/react-app embedded component (@cmdcolin)
• __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
  • #3731 Fix view menu going off screen in some cases (@cmdcolin)
• app-core
  • #3713 Fix centering of the ImportForm on SV inspector (@cmdcolin)

:memo: Documentation

• Other
  • #3752 Add storybook example for fetching features currently in view (@cmdcolin)
  • #3732 Add JBrowse R shiny app demo (@carolinebridge-oicr)
  • #3693 Remove package table from release blogposts (@cmdcolin)
• core, embedded-core, product-core
  • #3704 Organize autogenerated docs into categories (@cmdcolin)

: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
  • #3734 PileupRenderer refactor (@cmdcolin)
• app-core, core, product-core, web-core
  • #3717 More modularizing of shared app code (@cmdcolin)
• product-core
  • #3709 Silence console warn in CopyAndDelete test (@cmdcolin)
• app-core, core, embedded-core, product-core, text-indexing
  • #3701 Create app-core and embedded-core packages (@cmdcolin)
• core, product-core
  • #3661 Create packages/product-core containing shared code between the various products (@rbuels)

Committers: 6

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Robert Buels (@rbuels)
• Shivang Dwivedi (@studentshivang)
• @Lilas-w Done in 2.84s.

2.5.0 (2023-05-04)

:rocket: Enhancement

• Other
  • #3675 Use react-popper for tooltips in DotplotView (@cmdcolin)
  • #3637 Fix renderDelay not being applied to dynamicBlocks (@cmdcolin)
• 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
  • #3630 Fix flakiness of connection test (@cmdcolin)

: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
  • #3646 Refactor linear genome view storybook (@cmdcolin)

: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

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Robert Buels (@rbuels)
• @andrzejgrzelak

2.4.2 (2023-03-27)

:rocket: Enhancement

• core
  • #3604 Alignments tags description in feature details on mouseover (@cmdcolin)
• Other
  • #3586 Add authorization(internetAccount) support for Trix index files (@andrzejgrzelak)

: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

• Colin Diesh (@cmdcolin)
• @andrzejgrzelak

2.4.1 (2023-03-14)

: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

• #3571 Fixing link to PAG 2023 tutorial (@scottcain)

:house: Internal

• Other
  • #3567 Update github actions workflows to newer versions (@cmdcolin)
• __mocks__, core, text-indexing
  • #3557 Add additional lint rules from typescript-eslint and eslint-plugin-unicorn (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Scott Cain (@scottcain)

2.4.0 (2023-02-24)

:rocket: Enhancement

• Other
  • #3527 Breakpoint split view SVG export (@cmdcolin)
  • #3510 Allow configuring default display height (@cmdcolin)
• 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

• #3525 Fix missing grid ticks in dotplot (@cmdcolin)
• #3524 Fix loading session shares that have a plus sign in the sessionId (@cmdcolin)

:memo: Documentation

• #3532 Check website links in CI (@cmdcolin)
• #3507 Fix mygene.info demo track (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.3.4 (2023-02-01)

: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

• #3487 Storybook 7 (@cmdcolin)
• #3464 Add source file to config/state model docs (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

2.3.3 (2023-01-11)

: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

• #3448 Typescriptify some docusaurus website code (@cmdcolin)
• #3444 Human vs mouse synteny demo (@cmdcolin)

:house: Internal

• core
  • #3445 Typescriptify more tests (@cmdcolin)
  • #3443 Restore console mocks after running (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

2.3.2 (2022-12-20)

: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

• Colin Diesh (@cmdcolin)

2.3.0 (2022-12-15)

: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
  • #3396 Use prettier to word wrap markdown prose (@cmdcolin)
• 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
  • #3394 Simplify RPC watchWorker (@cmdcolin)
  • #3386 Fix warning when rendering circular chord displays with web worker RPC (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

2.2.2 (2022-12-06)

: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
  • #3359 Fix typos in codebase using typos-cli (@cmdcolin)

: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

• #3347 Reduce number of quickstart guides (@cmdcolin)

:house: Internal

• core
  • #3368 Create base "Dialog" component to standardize dialogs across codebase (@cmdcolin)
• text-indexing
  • #3344 fix yarn build error in Windows (@Lilas-w)

Committers: 2

• Colin Diesh (@cmdcolin)
• @Lilas-w

2.2.1 (2022-11-21)

: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

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.2.0 (2022-11-04)

:rocket: Enhancement

• Other
  • #3296 Add option to use OAuth "state" param in internet accounts (@garrettjstevens)
  • #3285 Use typescript version of @gmod/cram (@cmdcolin)
• 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

• core, text-indexing
  • #3278 Auto-generate docs (@cmdcolin)

:house: Internal

• #3310 Remove CacheProvider emotion cache (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Scott Cain (@scottcain)

2.1.7 (2022-10-20)

:bug: Bug Fix

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

Committers: 1

• Colin Diesh (@cmdcolin)

2.1.6 (2022-10-19)

: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
  • #3276 Allow using web worker RPC on embedded LGV (@cmdcolin)

:bug: Bug Fix

• core
  • #3266 Fix relative path loading of plugins (@cmdcolin)
  • #3269 Fix ability to rename session in web/desktop (@cmdcolin)
  • #3256 Fix tracks hanging in safari and polyfill for bigwig tracks (@cmdcolin)
• Other
  • #3274 Update bbi-js for bugfix on webpack 4 (@cmdcolin)
  • #3259 Fix issue with breakpoint split view using view before initialized (@cmdcolin)

:memo: Documentation

• #3255 Add more docs about color callbacks (@cmdcolin)

:house: Internal

• core
  • #3261 Fix for flaky test (@cmdcolin)

Committers: 3

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Scott Cain (@scottcain)

2.1.5 (2022-10-03)

: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
  • #3231 Fix theme coloring for components that use overrides e.g. accordion summary (@garrettjstevens)

:memo: Documentation

• #3193 Add desktop specific plugin tutorial (@carolinebridge-oicr)

:house: Internal

• Other
  • #3243 Add component test for circular genome view (@cmdcolin)
  • #3242 Fix flaky test in plugins/linear-genome-view (@cmdcolin)
• core
  • #3228 Improve TypeScript for queueDialog (@garrettjstevens)
  • #3224 More typescripting of plain js files (@cmdcolin)
  • #3207 Hardcoded block width of 800px on static blocks (@cmdcolin)
  • #3197 Use "temporaryAssemblies" to store read vs ref assemblies, and allow selecting "sessionAssemblies" in dropdown (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.1.4 (2022-09-16)

:bug: Bug Fix

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

Committers: 1

• Colin Diesh (@cmdcolin)

2.1.3 (2022-09-15)

: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
  • #3180 Improve adding assemblies internally, and use the assembly displayName in more places in the UI (@garrettjstevens)
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)

: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
  • #3170 Fix drawing inverted CIGAR segments on dotplot (@cmdcolin)
  • #3170 Fix drawing inverted CIGAR segments on dotplot (@cmdcolin)

:memo: Documentation

• #3138 Documentation overhaul (@carolinebridge-oicr)
• #3138 Documentation overhaul (@carolinebridge-oicr)

:house: Internal

• Other
  • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
  • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
  • #3165 Use more defaults in rollup plugins (@garrettjstevens)
• core
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
  • #3164 Typescript the QuickLRU module in @jbrowse/core (@cmdcolin)
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
  • #3164 Typescript the QuickLRU module in @jbrowse/core (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.1.1 (2022-08-25)

:rocket: Enhancement

• Other
  • #3152 Render CSQ and ANN fields in VCF feature details as data grids (@cmdcolin)
  • #3137 Make ideogram menu item similar to others (@garrettjstevens)
• core
  • #3159 Sequence search track (@cmdcolin)
  • #3132 Extend theme with module augmentation (@garrettjstevens)

: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

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.1.0 (2022-07-28)

: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
  • #3095 Add MUI exports to re-exports list (@garrettjstevens)
  • #3092 Fix use of embedded components with vite 3.0 using tsc to compile @jbrowse/core (@cmdcolin)

:memo: Documentation

• #3116 Add docs for multi-wiggle tracks (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.0.1 (2022-07-13)

:rocket: Enhancement

• core
  • #3089 Clarify error message when adapter has no features (@garrettjstevens)
  • #3084 Show a descriptive error if an adapter doesn't provide a sequence (@garrettjstevens)
  • #3071 Add ability to mouseover/click on synteny feature polygons in the linear synteny view (@cmdcolin)
• Other
  • #3081 Add ability to toggle gridlines on the LGV (@cmdcolin)

: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

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

2.0.0 (2022-07-07)

: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
  • #3072 Fix the display of inversions for MCScan alignments (@cmdcolin)
  • #3057 Fix export SVG crash on some BigWig tracks (@cmdcolin)
  • #3052 Fix negative value quantitative display in svg exports (@cmdcolin)
• 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

• #3067 Typescriptify some integration tests (@cmdcolin)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

1.7.11 (2022-06-22)

: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
  • #3042 Add fetch with proxy support to jbrowse CLI (@cmdcolin)
  • #3038 Display coordinates in overview scalebar when no cytoband available (@cmdcolin)
  • #3015 Add plaintext bed support with BedAdapter (@cmdcolin)

:bug: Bug Fix

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

:memo: Documentation

• #2831 Update commands for sorting GFF3 for tabix (@cmdcolin)
• #3018 Add desktop specific plugin example (@cmdcolin)
• #3022 Add example using embedded components with next.js (@cmdcolin)

:house: Internal

• core
  • #3035 Add typescripting to hierarchical track selector (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin)

1.7.10 (2022-06-13)

: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

• Other
  • #3021 Fix mouseover display of read name to alignments track (@cmdcolin)
  • #3012 Small fix to rankSearchResults logic (@cmdcolin)
  • #3009 Add jsdom to jbrowse-img to fix --noRasterize option (@cmdcolin)
• core
  • #3007 Fix read vs ref dotplot view (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• @andrzejgrzelak

1.7.9 (2022-06-02)

: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
  • #2994 Allow choosing filename for svg export (@cmdcolin)

:bug: Bug Fix

• core
  • #2989 Fix bezierCurveTo ponyfill on firefox (@cmdcolin)
• 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

• #2980 Remove errors related to test coverage in CI (@cmdcolin)

Committers: 4

• Adam Wright (@adamjohnwright)
• Colin Diesh (@cmdcolin)
• Teresa Martinez (@teresam856)
• Watal M. Iwasaki (@heavywatal)

1.7.8 (2022-05-20)

:rocket: Enhancement

• #2970 Draw indels in modifications/methylation mode (@cmdcolin)
• #2961 Add more visible pileup mismatches when zoomed out (@cmdcolin)
• #2960 Avoid performing a text index search if input looks like a locstring (@cmdcolin)
• #2954 Support in-memory GFF3 and GTF in JBrowse 1 connection (@garrettjstevens)
• #2947 Optimization for SNPCoverageAdapter and CRAM parsing (@cmdcolin)

: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

• #2946 Small doc updates (@cmdcolin)

:house: Internal

• #2955 Re-enable eslint autofix for prettier rules (@garrettjstevens)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

1.7.7 (2022-05-04)

:bug: Bug Fix

• #2941 Fix linear read vs ref hanging in v1.7.5 (@cmdcolin)

:house: Internal

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

Committers: 1

• Colin Diesh (@cmdcolin)

1.7.6 (2022-04-26)

:bug: Bug Fix

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

Committers: 1

• Colin Diesh (@cmdcolin)

1.7.5 (2022-04-26)

: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
  • #2684 Text-indexing in desktop (@teresam856)

: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

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Teresa Martinez (@teresam856)

1.7.4 (2022-04-19)

:bug: Bug Fix

• Other
  • #2925 Fix embedded vanillaJS/script tag usage of embedded components (@cmdcolin)
• core
  • #2923 Add babel/runtime to dependencies (@garrettjstevens)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

1.7.1 (2022-04-15)

:bug: Bug Fix

• core
  • #2917 Create tsconfig.build.json to add types to plugins/embedded components (@cmdcolin)
• Other
  • #2914 Manually polyfill fetch in @jbrowse/img (@cmdcolin)

:memo: Documentation

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

Committers: 1

• Colin Diesh (@cmdcolin)

1.7.0 (2022-04-14)

: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

• #2894 Add create-react-app v5 embedded component demos (@cmdcolin)
• #2830 Documentation comparing main app with embedded components (@carolinebridge-oicr)

: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
  • #2905 Use react-use-measure instead of react-use-dimensions (@cmdcolin)
  • #2646 Upgrade repository to use webpack 5/CRA 5 (@cmdcolin)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Robert Buels (@rbuels)

1.6.8 (2022-03-25)

:rocket: Enhancement

• Other
  • #2847 Add option to color all the letters on all the reads to the pileup renderer (@cmdcolin)
  • #2849 Avoid drawing intron subfeatures for gene glyphs (@cmdcolin)
  • #2835 Hide add track and connection menu items when using embedded component (@carolinebridge-oicr)
  • #2836 Display low-quality modifications in SNPCoverage renderer for MM tag (@cmdcolin)
• core
  • #2809 Optimizations for alignments tracks and BAM parsing (@cmdcolin)
  • #2828 Change calculation for number of webworkers for web/desktop (@cmdcolin)
  • #2829 Allow user to specify number of workers (@garrettjstevens)
  • #2775 New SVG gene glyph with directional arrows (@cmdcolin)

: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
  • #2841 Fix alignments tracks loading excessive data on chromosomes where no features exist (@cmdcolin)
  • #2829 Allow user to specify number of workers (@garrettjstevens)

Committers: 3

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

1.6.7 (2022-03-16)

:rocket: Enhancement

• #2820 Add optimization for BAM and unzip operations (@cmdcolin)

:bug: Bug Fix

• #2821 Fixup scroll on wiggle tracks with trackLabels->offset (@cmdcolin)
• #2819 Fix bug in desktop where first track gets stuck loading (@garrettjstevens)

Committers: 2

• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)

1.6.6 (2022-03-15)