Releases · GMOD/jbrowse-components

08 Mar 23:47

github-actions

v1.0.4

c6a5f12

Release v1.0.4

This release of JBrowse Web includes a great many small improvements and bug fixes, see the full changelog below.

Some particularly salient improvements include:

Better indications for insertions

The alignments track received a couple updates including "large insertion indicators" for large indels, and also an upside-down count of clipping or insertion events. There is also a triangular indicator plotted when the insertion/clip count exceeds a threshold at that position defaulted to 30% of reads

Click and drag the overview bar to "Get sequence"

Users can now download regions of sequence by selecting a region in the linear genome view and clicking "get sequence". See the demonstration video below:

You can also "get sequence" in the read vs reference view, which allows you to "get sequence" for the inserted bases or softclipped bases from a read alignment

A long-requested feature, implemented in #1588 by @teresam856!

Enhanced navigation of paired end reads and BND/TRA breakends

Feature detail panels for BND/TRA features, long split-alignments, and paired-end reads have links to navigate or popup of the breakpoint split views with their mates.

Implemented by @cmdcolin in #1701.

🚀 Enhancement

core
- #1758 Add ability to get stitched together CDS, protein, and cDNA sequences in feature details (@cmdcolin)
- #1721 Manually adjust feature height and spacing on alignments track (@cmdcolin)
- #1728 Add list of loaded plugins to the "About widget" (@rbuels)
- #1711 Add plugin top-level configuration (@teresam856)
- #1699 Add sequence track for both read and reference genome in the "Linear read vs ref" comparison (@cmdcolin)
- #1701 Add clickable navigation links to supplementary alignments/paired ends locations and BND/TRA endpoints in detail widgets (@cmdcolin)
- #1601 Add ability to color by per-base quality in alignment tracks (@cmdcolin)
- #1640 Move stats calculation to BaseFeatureAdapter (@cmdcolin)
- #1588 Add "Get sequence" action to LGV rubber-band (@teresam856)
Other
- #1743 Add color picker and choice of summary score style for wiggle track (@cmdcolin)
- #1763 Add a "CSS reset" to jbrowse-react-linear-genome-view to prevent parent styles from outside the component leaking in (@cmdcolin)
- #1756 Split alignments track menu items into "Pileup" and "SNPCoverage" submenus (@cmdcolin)
- #1742 Add ability to display crosshatches on the wiggle line/xyplot renderer (@cmdcolin)
- #1736 Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs (@cmdcolin)
- #1394 Add new menu items for show/hide feature labels, set max height, and set compact display mode (@cmdcolin)
- #1720 Standardize phred qual scaling between BAM and CRAM and add option to make mismatches render in a lighter color when quality is low (@cmdcolin)
- #1704 Add "Show all regions in assembly" to import form and make import form show entire region when refName selected (@cmdcolin)
- #1687 Threshold for indicators on SNPCoverage + inverted bargraph of interbase counts for sub-threshold events (@cmdcolin)
- #1695 Improve zoomed-out display of quantitative displays tracks when bicolor pivot is active (@cmdcolin)
- #1680 Add on click functionality to quantitative track features (@teresam856)
- #1630 Get column names from BED tabix files and other utils for external jbrowse-plugin-gwas support (@cmdcolin)
- #1709 Improve sorting and filtering in variant detail widget (@cmdcolin)
- #1688 Bold insertion indicator for large insertions on pileup track (@cmdcolin)
- #1669 Allow plain json encoding of the session in the URL (@cmdcolin)
- #1642 Enable locstring navigation from LGV import form (@teresam856)
- #1655 Add GFF3Tabix and BEDTabix inference to JB1 connection (@garrettjstevens)
- #1643 Add an offset that allows all wiggle y-scalebar labels to be visible (@cmdcolin)
- #1632 Displays warnings when receiving a session with custom callbacks (@peterkxie)
- #1615 Increase pileup maxHeight (@cmdcolin)
- #1624 GCContent adapter (@cmdcolin)
- #1614 Add insertion and clip indicators to SNPCoverage views (part of Alignments tracks) (@cmdcolin)
- #1610 Display error message from dynamodb session sharing error (@cmdcolin)

🐛 Bug Fix

Other
- #1777 Quick fix for block error (@cmdcolin)
- #1748 External plugins load after confirming config warning (@peterkxie)
- #1750 Fix pileup sorting when using string tag (@cmdcolin)
- #1747 Fix the position of the popup menu after rubberband select when there is a margin on the component e.g. in embedded (@cmdcolin)
- #1736 Fix CLI add-track --load inPlace to put exact contents into the config, add better CLI example docs (@cmdcolin)
- #1731 Fix alignment track ability to remember the height of the SNPCoverage subtrack on refresh (@cmdcolin)
- #1719 Fix for navigation past end of chromosome (@cmdcolin)
- #1698 Fix rendering read vs ref comparisons with CIGAR strings that use = sign matches (@cmdcolin)
- #1697 Fix softclipping configuration setting causing bases to be missed (@cmdcolin)
- #1689 Disable copy/delete menu items for reference sequence track (@teresam856)
- #1682 Fix parsing of BED and BEDPE files with comment header for spreadsheet view (@cmdcolin)
- #1679 Fix issue with using launching the add track widget on views that are not displaying any regions ([@t...

Assets 3

11 Jan 23:13

github-actions

v1.0.3

2ebe4b7

Release v1.0.3

This release of JBrowse Web includes several improvements and bug fixes, including:

Search and dropdown combined into single intuitive component on linear genome view
Big alignment track enhancements
- Added sort by tag to sorting options
- Added ability to color by preset options such as "base pair", "mapping quality", and "tag"
- Added ability to filter by preset options such as "read paired" and "read reverse strand"
Feature detail widget now shows subfeature details
Added --branch and --nightly flags for create and upgrade CLI commands
Improved admin server GUI
Additional track menu options for wiggle and SNP coverage tracks such as "autoscale", "log scale" and "histogram fill"
Improved build system for external plugins (check out our new plugin template at https://github.com/GMOD/jbrowse-plugin-template)

1.0.3 (2021-01-11)

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	https://www.npmjs.com/package/@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-gff3	https://www.npmjs.com/package/@jbrowse/plugin-gff3
@jbrowse/plugin-hic
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-view	https://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-menus
@jbrowse/plugin-spreadsheet-view
@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
- #1560 Provide a dialog to add extra genomic context for linear read vs. ref visualization (@elliothershberg)
- #1604 Add ability to filter for read name to the alignments filter dialog (@cmdcolin)
- #1599 Replace 'show all regions' with 'show all regions in assembly' (@cmdcolin)
- #1595 Admin server GUI enhancements (@elliothershberg)
- #1584 Restructure demo page and release cancer demo (@elliothershberg)
- #1579 Create --branch and --nightly flags for jbrowse create and jbrowse upgrade commands (@cmdcolin)
- #1575 Improve mobx-state-tree type validation errors (@cmdcolin)
- #1574 Make softclip indicator black if no seq available (@cmdcolin)
- #1554 Coloring options with simple color for tag (@peterkxie)
- #1565 Rename jbrowse cli add-track --type to --trackType (@cmdcolin)
- #1558 Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo (@cmdcolin)
- #1533 Display file headers in pre tag in about dialogs and bump @gmod/bam and @gmod/tabix package versions (@cmdcolin)
- #1541 Add more info about adding a PAF file to the synteny import form (@cmdcolin)
- #1509 Combine Search and Dropdown component on LGV (@teresam856)
- #1530 Add spreadsheet filter support for derived columns (@elliothershberg)
- #1483 Add session export to and import from file (@garrettjstevens)
- #1519 Add autoSql to the bigBed "About this track" dialog (@cmdcolin)
core
- #1531 Add track menu options for autoscale, log scale, histogram fill, setting min/max score, and zoom level/resolution for wiggle/snpcoverage tracks (@cmdcolin)
- #1473 Color, filter, and sort options for the alignments (@cmdcolin)
- #1576 Add location string to tooltip for wiggle and SNPCoverage tracks (@cmdcolin)
- #1529 Display subfeatures in feature details widget (@cmdcolin)
core, development-tools
- #1578 Update build system for external plugins (@garrettjstevens)

🐛 Bug Fix

Other
- #1608 Take into account offsetX of the rubberband on scalebar zooming (@cmdcolin)
- #1597 Fix crash when there are undefined references in the state tree e.g. when a track is deleted but still referred to by a session (@peterkxie)
- #1598 Disable 'copy to clipboard' while share url being generated (@peterkxie)
- #1589 Fix the display of trackhub registry results (@cmdcolin)
- #1573 Update hic-straw to fix error for hic files with many scaffolds (@cmdcolin)
- #1563 Remove softclip and hardclip from being counted as SNPs in the SNPCoverage (@cmdcolin)
- #1559 Avoid errors from breakpoint split view related to getBoundingClientRect on null track (@cmdcolin)
- #1540 Fix memory leak when side scrolling LGV blocks (@cmdcolin)
- #1534 Fix breakpoint split view showing too many connections for paired end ends (@cmdcolin)
- #1524 Move loading flag for spreadsheet import wizard to volatile to avoid it persisting across refresh (@cmdcolin)
- #1521 Add missing dep to react-linear-genome-view (@garrettjstevens)
core
- #1587 Fix positioning of scalebar tooltips, overview scalebar plotting, and refName label positioning when displaying many regions (@cmdcolin)
- #1547 Fix analytics crashing when using plugins (@cmdcolin)

📝 Documentation

#1594 Add GFF3 example to quickstart (@cmdcolin)
#1581 Add some features that are missing from jbrowse 2 to the feature comparison table (@cmdcolin)
#1558 Add docs for sequence track, variant track, launching synteny from dotplot, and add UCSC plugin to demo (@cmdcolin)
#1537 Add CONTRIBUTING.md with tips for getting started with codebase (@cmdcolin)

🏠 Internal

#1606 Upgrade @testing-library/react and improve test reliability (@cmdcolin)
#1555 Remove the TextDecoder/TextEncoder polyfill (@cmdcolin)
[#1522](https://gi...

Assets 3

02 Dec 18:37

github-actions

v1.0.2

5b0a7de

Release v1.0.2

This release addresses two main issues:

A bug introduced in v1.0.1 where the CLI command jbrowse create would not
download the latest version of JBrowse Web.
A fix for a problem that prevented @jbrowse/react-linear-genome-view (first
released in v1.0.1) from working properly.

Several other bug fixes and improvements are also included. See details below.

v1.0.2 (2020-12-02)

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	https://www.npmjs.com/package/@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-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

core
- #1513 Add a custom scrollbar that overrides the auto-hiding behavior of scrollbars on OSX (@elliothershberg)

🐛 Bug Fix

Other
- #1514 react-linear-genome-view bug fixes (@garrettjstevens)
- #1517 Fix the use of filtering display on desktop (@cmdcolin)
- #1512 Fix setting maxDisplayedBpPerPx for pileup display, helps prevent too large an area from being rendered (@cmdcolin)
- #1442 Change track selector togglebutton to normal button (@cmdcolin)
- #1506 Fix horizontally flipped translation frames position (@cmdcolin)
- #1501 Fix CLI to allow jbrowse create to download newer monorepo tag format (@cmdcolin)
core
- #1505 Fix loading of local files in jbrowse-desktop (@cmdcolin)

Committers: 3

Colin Diesh (@cmdcolin)
Elliot Hershberg (@elliothershberg)
Garrett Stevens (@garrettjstevens)

Assets 3

25 Nov 21:58

github-actions

v1.0.1

ffbe57d

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
- #1491 Fix ability to add a PAF synteny track with add-track (@cmdcolin)
- #1470 Avoid rendering the literal string 'null' in the feature details (@cmdcolin)
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)