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v2.0.1 Release

· 2 min read

We are pleased to announce 2.0.1

This release features the ability to mouseover and click synteny alignments on the linear synteny view

If there are base level alignments, either from the read vs ref view or e.g. a PAF file generated with minimap -c (outputs CIGAR), then you can also mouse over to get information about the particular part of that alignment e.g. the CIGAR string

Figure showing a mouseover inside a deletion in the read vs ref view

This release also has some other small fixes and improvements, see release notes!

Downloads​

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.

2.0.1 (2022-07-13)​

🚀 Enhancement​

🐛 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​

v2.0.0 Release

· 2 min read

We are pleased to release v2.0.0! This is a major version milestone, but it does not have a huge number of changes. Instead, the major change that resulted in becoming v2.0.0 was the upgrade of many of our dependencies including

  • material-ui v4 -> v5
  • mobx-state-tree v3.14.1 -> v5
  • mobx-react v6 -> v7
  • mobx v5 -> v6

Therefore, to help users that may have been relying on library versions like this, it is safer to make the version a major bump. If you run into any issues with this upgrade, let us know and we can help

Some notable improvements:

  • This release improves bundle sizes for users of embedded components, by adding ESM builds to NPM. This can reduce the initial load of a webpage using e.g. @jbrowse/react-linear-genome-view by about 55% (1.4MB gzipped js->770kb gzipped js)

Downloads​

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.

2.0.0 (2022-07-07)​

🚀 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 Fix​

  • Other
    • #3072 Fix the display of inversions for MCScan alignments (@cmdcolin)
    • #3074 Fix the display of deletions vs insertions being backwards in synteny view with CIGAR strings (@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)

🏠 Internal​

Committers: 2​

v1.7.11 Release

· 2 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 because it only really was needed in niche circumstances. This will improve the ease of installing packages like @jbrowse/react-linear-genome-view.

Downloads​

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.

1.7.11 (2022-06-22)​

🚀 Enhancement​

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

🐛 Bug Fix​

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

📝 Documentation​

🏠 Internal​

  • core

Committers: 1​

v1.7.10 Release

· 3 min read

We are pleased to present the latest JBrowse 2 release!

This has some great new features including

Feature detail formatter​

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 confirm​

Large track menus no longer disappear off the screen​

Before

After

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

Downloads​

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.

1.7.10 (2022-06-13)​

🚀 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 Fix​

Committers: 3​

v1.7.9 Release

· 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)

Downloads​

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.

1.7.9 (2022-06-02)​

🚀 Enhancement​

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

🐛 Bug Fix​

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

🏠 Internal​

Committers: 4​

v1.7.8 Release

· 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

Downloads​

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.

1.7.8 (2022-05-20)​

🚀 Enhancement​

🐛 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)

📝 Documentation​

🏠 Internal​

Committers: 2​

v1.7.7 Release

· 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

Downloads​

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.

1.7.7 (2022-05-04)​

🐛 Bug Fix​

🏠 Internal​

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

Committers: 1​

v1.7.6 Release

· 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!

Downloads​

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.

1.7.6 (2022-04-26)​

🐛 Bug Fix​

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

Committers: 1​

v1.7.5 Release

· 2 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)

Downloads​

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.

1.7.5 (2022-04-26)​

🚀 Enhancement​

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

🐛 Bug 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​

v1.7.4 Release

· One 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

Downloads​

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.

1.7.4 (2022-04-19)​

🐛 Bug Fix​

Committers: 2​