Release v1.0.1
This release of JBrowse Web includes several improvements and bug fixes,
including:
- A new sequence track renderer that includes translation frames
- The addition of session connections
- A new track selector icon
- Improvements to feature details widgets
- And more! See details below.
To install JBrowse 2 for the web, you can download the release ZIP, 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.
v1.0.1 (2020-11-25)
Packages in this release
| Package | Download |
|---|---|
| @jbrowse/core | https://www.npmjs.com/package/@jbrowse/core |
| @jbrowse/development-tools | https://www.npmjs.com/package/@jbrowse/development-tools |
| @jbrowse/plugin-alignments | https://www.npmjs.com/package/@jbrowse/plugin-alignments |
| @jbrowse/plugin-bed | https://www.npmjs.com/package/@jbrowse/plugin-bed |
| @jbrowse/plugin-breakpoint-split-view | |
| @jbrowse/plugin-circular-view | |
| @jbrowse/plugin-config | https://www.npmjs.com/package/@jbrowse/plugin-config |
| @jbrowse/plugin-data-management | https://www.npmjs.com/package/@jbrowse/plugin-data-management |
| @jbrowse/plugin-dotplot-view | |
| @jbrowse/plugin-filtering | |
| @jbrowse/plugin-gff3 | https://www.npmjs.com/package/@jbrowse/plugin-gff3 |
| @jbrowse/plugin-hic | |
| @jbrowse/plugin-legacy-jbrowse | |
| @jbrowse/plugin-linear-comparative-view | |
| @jbrowse/plugin-linear-genome-view | https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view |
| @jbrowse/plugin-lollipop | |
| @jbrowse/plugin-menus | |
| @jbrowse/plugin-protein | |
| @jbrowse/plugin-rdf | |
| @jbrowse/plugin-sequence | https://www.npmjs.com/package/@jbrowse/plugin-sequence |
| @jbrowse/plugin-spreadsheet-view | |
| @jbrowse/plugin-sv-inspector | |
| @jbrowse/plugin-svg | https://www.npmjs.com/package/@jbrowse/plugin-svg |
| @jbrowse/plugin-trackhub-registry | |
| @jbrowse/plugin-variants | https://www.npmjs.com/package/@jbrowse/plugin-variants |
| @jbrowse/plugin-wiggle | https://www.npmjs.com/package/@jbrowse/plugin-wiggle |
| @jbrowse/cli | https://www.npmjs.com/package/@jbrowse/cli |
| @jbrowse/desktop | |
| @jbrowse/protein-widget | |
| @jbrowse/react-linear-genome-view | https://www.npmjs.com/package/@jbrowse/react-linear-genome-view |
| @jbrowse/web |
🚀 Enhancement
- Other
- #1462 Allow importing gzip and bgzip files in the spreadsheet and SV inspector (@cmdcolin)
- #1460 Add support for more bigBed subtypes and fallback for unsupported types (@peterkxie)
- #1455 Add the ability to use connection across refreshes in jbrowse-web using session connections (@peterkxie)
- #1439 1381 improve assembly add form (@elliothershberg)
- #1433 Make add track warning a bit more lenient (@garrettjstevens)
- #1420 Add the assembly manager feature to jbrowse-desktop (@elliothershberg)
core- #1458 Add three frame translation to the sequence track (@cmdcolin)
- #1453 Change "Factory reset" to "Reset session" in jbrowse-web (@teresam856)
- #1441 New icon for the track selector (@cmdcolin)
- #1438 Improve assembly loading time by moving to main thread (@cmdcolin)
- #1434 Create separate config schema for ReferenceSequenceTrack (@elliothershberg)
🐛 Bug Fix
core- Other
- #1489 Fix long read vs ref CIGAR rendering for horizontally flipped synteny view (@cmdcolin)
- #1460 Add support for more bigBed subtypes and fallback for unsupported types (@peterkxie)
- #1472 Wait on assemblies that are being tracked by the assemblyManager only (@cmdcolin)
- #1466 Avoid rendering the display and renderer settings in the about this track dialog (@cmdcolin)
- #1461 Fix usage of jbrowse-cli on node 10.9 related to fs.promises (@cmdcolin)
- #1452 Bug: search box disappears from LGV header on smaller widths (@teresam856)
- #1432 Make global variables window.JBrowseSession and window.JBrowseRootModel available in jbrowse-web (@teresam856)
- #1431 Fix connection tracks not showing up in track selector (@garrettjstevens)
- #1428 Fix the listVersions behavior of the jbrowse-cli returning duplicate entries (@cmdcolin)
- #1422 Fix crash from empty ALT field in VCF (@cmdcolin)
- #1413 Fix ability to add CRAM tracks using the web based add-track GUI (@cmdcolin)
📝 Documentation
- #1435 Updates to quickstart guides (@garrettjstevens)
🏠 Internal
- Other
- #1437 Use lerna-changelog for changelog generation (@cmdcolin)
- #1465 Establish minimum node version of 10.4 for using jbrowse-cli tools (@cmdcolin)
- #1454 Fix GH workflow build (@elliothershberg)
- #1448 Move building and testing from Travis to GitHub Workflow (@garrettjstevens)
- #1450 Fix website build (@garrettjstevens)
core- #1468 Have assembly manager get plugin manager from factory function args (@garrettjstevens)
Committers: 5
- Colin Diesh (@cmdcolin)
- Elliot Hershberg (@elliothershberg)
- Garrett Stevens (@garrettjstevens)
- Teresa Martinez (@teresam856)
- @peterkxie