Release v4.1.1
Hello all,
This is a minor release but contains a couple great new features, and some important bugfixes. Please see the release notes below
Local files are preserved even after page refresh in jbrowse-web
When users of jbrowse-web open files from their local machine, it can continue to work after page refresh. This is currently a Chrome only feature facilitated by the FileSystemFileHandle API https://developer.mozilla.org/en-US/docs/Web/API/FileSystemFileHandle
Add advanced track configuration via the URL bar
Previously, users could launch tracks by supplying a list of trackIds in the URL e.g. &tracks=track1,track2. Now, users can supply an array of JSON params https://jbrowse.org/jb2/docs/urlparams/#advanced-track-configuration
Add linkage disequilibrium viewer
In an effort to expand the utility of our variant visualization capabilities, we integrated a built-in linkage disequilibrium viewer for multi-sample variant tracks. This can load data from multi-sample variant files or PLINK output files. This can plot r^2 and D' with a variety of visual customization options
See the full changelog below for more info
bug
- Minor fixes for genbank and gff3 file export (#5435) @cmdcolin
- Fix issues with large VCF files not displaying in v4.0.4 (#5432) @cmdcolin
- Add testing for remote file fetching in text-index (#5429) @cmdcolin
- Fix text-index from remote gz file. (#5427) @Yihuki
enhancement
- Add stack trace to jbrowse desktop text indexing failures (#5436) @cmdcolin
- Add config.json slots for multi-sample variant displays (#5434) @cmdcolin
- Add examples of using the Core-preProcessConfig extension point (#5433) @cmdcolin
- Bump to @gmod/cram v8 for qual speed and memory optimization (#5430) @cmdcolin
- Allow supplying initial display parameters when using URL query param API (#5426) @cmdcolin
- Allow custom jexl functions to be used in filters (#5425) @cmdcolin
- Add type:"module" to package.json's to complete ESM conversion (#5422) @cmdcolin
- Add testing for electron app using windows github action runner and fix text indexing on windows (#5421) @cmdcolin
- Create system for visualizing linkage disequilibrium from VCF and PLINK output files (#5420) @cmdcolin
- Add ability to reload local files across page using FileSystemFileHandle API (#5419) @cmdcolin
- Add re-exports to enable embedded apps to use webworkers after v4 (#5418) @cmdcolin
