@jbrowse/plugin-arc - npm Package Versions

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