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ยท 3 min read

We are excited to announce v1.7.11!

This release has some relatively small fixes to the UI, docs, and examples. For developers, they may notice that we have removed node-canvas due to it's need for having extra system dependencies, and becuase it only really was needed in niche circumstances. This will improve the ease of installing packages like @jbrowse/react-linear-genome-view.

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.11 (2022-06-22)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bedhttps://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-viewhttps://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-jobs-management
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿš€ Enhancementโ€‹

  • 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

๐Ÿ› Bug Fixโ€‹

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

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

  • core

Committers: 1โ€‹

ยท 4 min read

We are pleased to present the latest JBrowse 2 release!

This has some great new features including

Feature detail formatterโ€‹

Here is an example which adds a link to the "Name" panel in the feature details. It uses the jexl callback that returns an object with keys for each field to modify (e.g. the key name is used here). See

{
"type": "FeatureTrack",
"trackId": "ncbi_gff_hg19_2",
"name": "NCBI RefSeq",
"formatDetails": {
"feature": "jexl:{name:'<a href=https://google.com/?q='+feature.name+'>'+feature.name+'</a>'}"
},
"assemblyNames": ["hg19"],
"adapter": {
"type": "Gff3TabixAdapter",
"gffGzLocation": {
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz"
},
"index": {
"location": {
"uri": "https://s3.amazonaws.com/jbrowse.org/genomes/hg19/ncbi_refseq/GRCh37_latest_genomic.sort.gff.gz.tbi"
}
}
}
}

Example screenshot

See https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels for more info

Clearer configuration panel with explicit "Add item" button with "OK"/"Cancel" to confirmโ€‹

Large track menus no longer disappear off the screenโ€‹

Before

After

See also the "Copy config" button to download the config

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.10 (2022-06-13)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿš€ Enhancementโ€‹

  • 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)

๐Ÿ› Bug Fixโ€‹

Committers: 3โ€‹

ยท 2 min read

We are pleased to present v1.7.9!

This release features several bugfixes and improvements submitted by community members, including a CLI fix when specifying --indexFile with CSI files, and a new feature to get FASTA metadata from an external file.

Additionally, we have switched to canvas2svg for SVG exports, which can now handle more sophisticated operations like bezierCurves (used for sashimi-style arc in RNA-seq data), and circles (used by jbrowse-plugin-gwas)

Before (note bad intron and lack of arcs rendered on bottom track)

After (fixed intron rendering and arcs)

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.9 (2022-06-02)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿš€ Enhancementโ€‹

  • 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

๐Ÿ› Bug Fixโ€‹

๐Ÿ  Internalโ€‹

Committers: 4โ€‹

ยท 2 min read

We are happy to announce v1.7.8

Some highlights include

  • ~20% speed improvement for CRAM data
  • bugfix for filter-by being broken on alignments tracks in v1.7.0-v1.7.7
  • bugfix for certain methylation/modifications being drawn incorrectly on alignments tracks
  • bugfix for the "Open" button not navigating to the correct location on the LGV import form
  • improved visualization of indels in methylation/modifications mode on alignments tracks
  • skip text index query if the input is a loc string, resulting in quicker navigation

Screenshots showing the new viewing of indels when viewing methylation

Before

After

See the release notes for details

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.8 (2022-05-20)โ€‹

Packages in this release

PackageDownload
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

  • #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)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

Committers: 2โ€‹

ยท One min read

This is a small bugfix release, where in v1.7.5-1.7.6 the read vs ref and sequence panels in the feature details failed to load

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.7 (2022-05-04)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-linear-comparative-view
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿ› Bug Fixโ€‹

๐Ÿ  Internalโ€‹

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

Committers: 1โ€‹

ยท One min read

This fixes a bug that affected v1.7.0-v1.7.5 in which CRAM, TwoBit, and other file types would not load on jbrowse-desktop. This was due to the upgrade to webpack 5/CRA5, but is fixed in this release!

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.6 (2022-04-26)โ€‹

Packages in this release

PackageDownload
@jbrowse/desktop

๐Ÿ› Bug Fixโ€‹

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

Committers: 1โ€‹

ยท 3 min read

We are pleased to present the release of v1.7.5

This release includes two major improvements

  • Ability to index tracks for searching by gene names in JBrowse Desktop. This let's users choose per-track indexes in the add track widget interactively, or index them after-the-fact using the track menu.
  • Removed serialization of BAM/CRAM features for pileup tracks which brings large performance benefits for jbrowse-web and jbrowse-desktop. Previously, all the BAM/CRAM features were serialized across the RPC boundary in jbrowse-web and jbrowse-desktop, but this was an expensive and memory intensive operation. Now, the BAM/CRAM features are not serialized, but the main thread has to manually request any data it needs from the worker after rendering (e.g. when we click a feature).

Figure showing the "Index track" option in the track menu of JBrowse Desktop

Figure showing the "Index track" option in the add track widget of JBrowse Desktop

Figure showing performance improvement of the noserialize improvement compared with v1.7.4, which brings the webworker performance in line with the embedded app (which does no serialization)

This release also fixes a bug with using trix indexes created by jbrowse text-index in v1.7.0-v1.7.4 (with the adjustable prefix size)

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.5 (2022-04-26)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/text-indexing
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-bedhttps://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-jobs-management
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-text-indexing
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿš€ Enhancementโ€‹

  • core
    • #2885 Reduce serialization overhead on alignments tracks and access feature details asynchronously (@cmdcolin)
  • Other
  • core, text-indexing

๐Ÿ› Bug Fixโ€‹

  • #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: 3โ€‹

ยท 2 min read

This is a small patch release that fixes our UMD builds for embedded components fixes the @babel/runtime dependency in some npm packages

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.4 (2022-04-19)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bedhttps://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-viewhttps://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿ› Bug Fixโ€‹

Committers: 2โ€‹

ยท One min read

This is a release fixed some small issues with using typescript in the embedded components

See https://github.com/GMOD/jbrowse-components/releases/tag/v1.7.0 for the latest feature-set

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

Packages in this release

ยท 4 min read

We are excited to announce the latest JBrowse release! This has many great features including

  1. Floating feature labels, so if you are zoomed into the middle of a gene, the feature label hangs out alongside it on the left side of the screen! The results may not be pixel perfect in all cases (reverse complement labels can end up overlapping other features for example) but we hope this helps you see the labels for features that extend off the screen!

    Figure showing the feature labels floating alongside gene even when you are zoomed into the feature

  2. Upgraded build system for jbrowse-web and jbrowse-desktop to webpack 5, and added examples of using webpack 5 with embedded components. Webpack 5 results in smaller build sizes for jbrowse-web. For a typical session, amount of .js downloaded with gzip enabled in v1.6.9 is ~1.4MB, in v1.7.0 ~900kb (-500kb smaller). Without gzip enabled v1.6.9 4.8MB, v1.7.0 2.5MB (-2MB smaller). The result is largely due to better webworker bundling. See https://jbrowse.org/jb2/docs/embedded_components/ for webpack 5 examples in embedded components

  3. Optimizations and improved visualization of paired-end reads in the breakpoint split view

  4. Optimized linear synteny renderings with long CIGAR strings. These optimizations help viewing large alignments such as the CHM13-T2T-v2.0 assembly vs hg38 PAF file from https://github.com/marbl/CHM13#downloads (example here https://jbrowse.org/code/jb2/main/?config=test_data%2Fconfig_demo.json&session=share-0qD2-d_k4K&password=GF8Sk)

  5. The "Assembly selector" dropdown box now remembers your last selection, so you can more easily return to your genome of interest

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, or you can use the JBrowse CLI to automatically download the latest version. See the JBrowse web quick start for more details.

See "Packages in this release" in the changelog for links to packages published on NPM.

1.7.0 (2022-04-14)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bedhttps://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-view
@jbrowse/plugin-circular-viewhttps://www.npmjs.com/package/@jbrowse/plugin-circular-view
@jbrowse/plugin-comparative-adapters
@jbrowse/plugin-confighttps://www.npmjs.com/package/@jbrowse/plugin-config
@jbrowse/plugin-data-managementhttps://www.npmjs.com/package/@jbrowse/plugin-data-management
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-gff3https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-grid-bookmarkhttps://www.npmjs.com/package/@jbrowse/plugin-grid-bookmark
@jbrowse/plugin-gtfhttps://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-lollipop
@jbrowse/plugin-menus
@jbrowse/plugin-protein
@jbrowse/plugin-rdf
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-sv-inspector
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trackhub-registry
@jbrowse/plugin-trixhttps://www.npmjs.com/package/@jbrowse/plugin-trix
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
jbrowse-predefined-sessions
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿš€ Enhancementโ€‹

  • 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)

๐Ÿ› Bug Fixโ€‹

  • 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)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

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

Committers: 3โ€‹