92 posts tagged with "jbrowse 2"

v3.0.3 Release

February 13, 2025 · One min read

Fixes modifications drawing bug in v3.0.2

Downloads

v3.0.3

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.3

Done in 0.44s.

v3.0.2 Release

February 13, 2025 · 2 min read

This release mostly has small bugfixes and minor improvements

Fix for some CRAM files that use "archival" bzip2 codecs
Change multi-variant viewer to use a blue color for the "major ALT allele" rather than just ALT===1
Use assembly "displayName" in view headers
Group transcripts from GTF files into gene level features
Improved ?hubURL behavior to load defaultLocation, assembly names
Handle random color generation for >10 categories in the multi-variant viewer

Downloads

v3.0.2

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.2

3.0.2 (2025-02-13)

🚀 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 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)

📝 Documentation

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

🏠 Internal

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

Committers: 2

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

v3.0.1 Release

January 30, 2025 · One min read

This release fixes the vanillajs build for the linear genome view the hover genotype feature in v3.0.0

Downloads

v3.0.1

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.1

Done in 0.69s.

This release announces v3.0.0 of JBrowse 2. It is not at all a dramatic change like the JBrowse 1 -> JBrowse 2 transition, it's much more incremental, and in fact, you can go on calling it JBrowse 2...as a point of comparison, ggplot2 is on v3.5.1 right now :)

We decided to make a major bump due to some small "breaking" changes that could affect plugin and embedded library users in particular.

But for most users, this release should have nothing but the usual bugfixes and improvements! And there are a lot of these!

Without further ado, here are some highlights!

Improved rendering of phased VCF in multi-variant view

Phased variants offer a unique opportunity to see which parent particular variants came from. To help this, we added a new "phased" rendering mode to the multi-variant renderings, that takes phased VCF and renders each phase as an individual row. This allows users to effectively see the entire row as a haplotype, and can be used to help visualize trio VCF to find parent of origin

Screenshot From 2025-01-25 15-03-21 Screenshot showing the "phased mode" for a trio VCF

Screenshot showing how to access the phased rendering mode

Rendering of phase-sets

This could be more or less uncommon depending on your work, but for incompletely phased variant calls you will see "phased sets" (PS tag in genotypes). We color each set a random color

Screenshot showing phase set rendering of a phased VCF. This is nearly completely phased so just showing green, but each phase set would get a unique color. The black entries are unphased variants (which could be filtered out, but this is not done currently)

Rendering polyploids in the multi-variant view

Screenshot showing the "polyploid" rendering of the multi-variant display.

Polyploid variant calls can look like 0/2/./1 indicating one match to the reference (0), two alts (1,2), and one missing call (.).

Yellow indicates missingness
Grey indicates reference
Blue indicates the ALT===1
Red is ALT!==1

Each of these is a spectrum that increases in darkness, so darker blue indicates more ALT===1, darker red indicates more ALT!==1, darker yellow is more uncalled, etc.

Adding sample metadata to VCF from an external TSV

Screenshot showing multi-sample matrix display, with the population colors coming from a "sample TSV" file. The below config shows the samplesTsvLocation config, the first column should match the sample name in the VCF

Example TSV

name	population
HG01879	ACB
HG01880	ACB
HG01881	ACB
HG01882	ACB
HG01883	ACB
HG01884	ACB

Config

{
  "type": "VariantTrack",
  "trackId": "1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf",
  "name": "1kGP_high_coverage_Illumina.chr1.filtered.SNV_INDEL_SV_phased_panel.vcf",
  "assemblyNames": ["hg19"],
  "adapter": {
    "type": "VcfTabixAdapter",
    "vcfGzLocation": {
      "uri": "https://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz"
    },
    "index": {
      "location": {
        "uri": "https://ftp-trace.ncbi.nlm.nih.gov/1000genomes/ftp/release/20130502/ALL.chr1.phase3_shapeit2_mvncall_integrated_v5a.20130502.genotypes.vcf.gz.tbi"
      }
    },
    "samplesTsvLocation": {
      "uri": "https://jbrowse.org/genomes/hg19/1000g.sorted.csv.gz"
    }
  }
}

Improved UI for opening synteny tracks

It has always been challenging for end users to open synteny tracks

To help with this, we now support adding synteny tracks via the default "Add track" workflow, and make it easier to specify the query and target assembly names. We also added a similar UI change to the "Linear synteny view" import form

Screenshot showing the default add track workflow with new UI for choosing target and query assemblies for PAF tracks

Screenshot showing the add track workflow in the "Linear synteny view" import form, also showing new UI for choosing query and target assmblies

New "turbo zoom" buttons

In working with users, we noticed people having to click the zoom buttons or fiddle with the slider a lot. To aid this, we added a small dropdown for quickly doing 10x, 50x, and 100x zooms

For developers: some "breaking" changes

We changed the "filehandle" type used in data adapters. We now use generic-filehandle2 which is simpler and does not require a node.js polyfill on the web
Upgrading React 18 -> React 19 in our main webapp. This drops support for React 17, and may have some other implications

If you are a plugin or embedded user, and experience problems with upgrading, let us know!

Downloads

v3.0.0

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.

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.0