Releases: GMOD/jbrowse-components
Release v2.0.0
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)
🚀 Enhancement
- Other
text-indexing__mocks__,core,text-indexing
🐛 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
🏠 Internal
Committers: 2
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Release v1.7.11
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.
🚀 Enhancement
core- Other
🐛 Bug Fix
📝 Documentation
- #2831 Update commands for sorting GFF3 for tabix (@cmdcolin)
- #3018 Add desktop specific plugin example (@cmdcolin)
- #3022 Add example using embedded components with next.js (@cmdcolin)
🏠 Internal
Committers: 1
- Colin Diesh (@cmdcolin)
Release v1.7.10
We are pleased to present the latest JBrowse 2 release!
This has some great new features including
- Feature detail formatters - add callback to add links or other customizations
to the feature details panels (see
https://jbrowse.org/jb2/docs/config_guide/#customizing-feature-details-panels
for more info) - Session URL formats for loading spreadsheet, SV inspector, and linear and
dotplot synteny views (see https://jbrowse.org/jb2/docs/urlparams/ for details) - You can enter "chr1 100 200" to navigate to "chr1:100-200" as a simple way to
copy from a bed file or similar
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
Automatically generate clickable links for data files in About track dialog
See also the "Copy config" button to download the config
🚀 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
🐛 Bug Fix
- Other
core
Committers: 3
- Caroline Bridge (@carolinebridge-oicr)
- Colin Diesh (@cmdcolin)
- @andrzejgrzelak
Release v1.7.9
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)
🚀 Enhancement
core- Other
- #2994 Allow choosing filename for svg export (@cmdcolin)
- #2968 Add FASTA metadata location to BgzipFastaAdapter and IndexFastaAdapter configuration (@adamjohnwright)
🐛 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
- Adam Wright (@adamjohnwright)
- Colin Diesh (@cmdcolin)
- Teresa Martinez (@teresam856)
- Watal M. Iwasaki (@heavywatal)
Release v1.7.8
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
🚀 Enhancement
- #2970 Draw indels in modifications/methylation mode (@cmdcolin)
- #2961 Add more visible pileup mismatches when zoomed out (@cmdcolin)
- #2960 Avoid performing a text index search if input looks like a locstring (@cmdcolin)
- #2954 Support in-memory GFF3 and GTF in JBrowse 1 connection (@garrettjstevens)
- #2947 Optimization for SNPCoverageAdapter and CRAM parsing (@cmdcolin)
🐛 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
- #2955 Re-enable eslint autofix for prettier rules (@garrettjstevens)
Committers: 2
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
Release v1.7.7
This is a small bugfix release, where in v1.7.0-1.7.6 the read vs ref and
sequence panels in the feature details failed to load
🐛 Bug Fix
🏠 Internal
Committers: 1
- Colin Diesh (@cmdcolin)
Release v1.7.6
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!
Release v1.7.5
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)
🚀 Enhancement
core- Other
core,text-indexing- #2684 Text-indexing in desktop (@teresam856)
🐛 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
- Colin Diesh (@cmdcolin)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
Release v1.7.4
This is a small patch release that fixes our UMD builds for embedded components fixes the @babel/runtime dependency in some npm packages
For the latest feature set see https://github.com/GMOD/jbrowse-components/releases/tag/v1.7.0
Release v1.7.3
This is a release that fixed issues for users of the embedded apps and follows from a botched release of v1.7.2 on npm
See https://github.com/GMOD/jbrowse-components/releases/tag/v1.7.0 for the latest feature-set