@jbrowse/cli - npm Package Versions

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