Release v1.5.2

[garrettjstevens]

We're excited to present some great new features and performance improvements in v1.5.2!

New arc display type

A new display type has been added for drawing arcs. The color, thickness, height, label, and caption of the arcs can be customized.

New plugin build system

We've re-worked the system used by developers to build external plugins for more stability and flexibility. The current plugin build system will continue to work, but if you want to check out how the new template works, check out the JBrowse Plugin Template.

Storybook docs added for Circular Genome View React component

Find them linked under @jbrowse/react-circular-genome-view here.

Performance improvements

The alignments track now has 25% faster speed on most datasets and particularly on deep short read sequencing, it can be up to 10x faster.

Check out the release notes for more!

1.5.2 (2021-12-20)

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-arc
@jbrowse/plugin-authentication
@jbrowse/plugin-bed	https://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-breakpoint-split-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-gtf	https://www.npmjs.com/package/@jbrowse/plugin-gtf
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowse	https://www.npmjs.com/package/@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-menus
@jbrowse/plugin-sequence	https://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svg	https://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-trix	https://www.npmjs.com/package/@jbrowse/plugin-trix
@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/img	https://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-view	https://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-view	https://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

🚀 Enhancement

• Other
  • #2579 Add help text and help dialog for the RefNameAutocomplete (@cmdcolin)
  • #2553 Add sashimi-style arcs for RNA-seq type skips on SNPCoverage display (@cmdcolin)
  • #2552 Change border on non-cytoband OverviewScaleBar visible region back to blue and cytoband OverviewScaleBar to a little lighter fill (@cmdcolin)
  • #2509 Implement prop interface for providing arbitrary user-defined glyphs to SvgFeatureRenderer (@hextraza)
  • #2485 Only use one button, "Go", in text search ambiguous results dialog (@cmdcolin)
  • #2501 Add a tooltip to desktop session path so you can see the full path if it's cut off (@garrettjstevens)
• core
  • #2580 Make core snackbar notifications module with auto-dismissing info/success level notifications (@cmdcolin)
  • #2534 New display type for drawing arcs (@carolinebridge-oicr)
  • #2590 Add more exports that can be used by plugins (@garrettjstevens)
  • #2578 Add layouts code to core re-exports (@garrettjstevens)
  • #2523 Performance optimizations for alignments tracks, particularly those with many short reads (@cmdcolin)
  • #2500 Add RenderProps to core/pluggableElementTypes export (@garrettjstevens)
• core, development-tools
  • #2487 Add support for additional types of plugin formats (commonjs, esm) to allow access to node modules on jbrowse desktop (@garrettjstevens)

🐛 Bug Fix

• Other
  • #2594 Fix infinite loop bug while searching certain strings and handle multi-word searches better (@cmdcolin)
  • #2589 Fix occasional failures observed from running text-index command (@cmdcolin)
  • #2583 Fix for alignments track base modifications display regarding skipped bases on Mm tag (@cmdcolin)
  • #2556 Fix ability to access BigWig tracks on http basic auth for some cases (@cmdcolin)
  • #2577 Fix ability to use --indexFile on VCF/GFF tabix and CRAM files and add plaintext VCF, GFF, GTF support to add-track CLI (@cmdcolin)
  • #2521 Fix ability to search for tracks with parentheses in tracklist (@cmdcolin)
  • #2512 Fix [object Window] issue in alignment read vs reference dialog (@cmdcolin)
  • #2499 Add missing dependency to CLI (@garrettjstevens)
• core
  • #2585 Fix ability to use "Color by methylation" on files that require refname renaming (@cmdcolin)
  • #2517 Remove aborting on adapter loading process to fix some tracks getting stuck in infinite loading state (@cmdcolin)
  • #2564 Start looking for parents with parent, not self in findParentThat (@garrettjstevens)
  • #2563 Restore ability to load plugins from relative URL (@garrettjstevens)
  • #2533 Fix drawer widget minimized button being unclickable when overlapping with a view (@cmdcolin)

📝 Documentation

• #2522 Add circular genome view storybook (@cmdcolin)
• #2508 Update docs for embedded components (@teresam856)
• #2495 Improve organization on docs landing page (@cmdcolin)

🏠 Internal

• core
  • #2597 Fix flaky tests related to auth and canvas image snapshots (@cmdcolin)
  • #2504 Spreadsheet change jbrequire to es6 imports (@cmdcolin)

Committers: 6

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• Peter Xie (@peterkxie)
• Sebastian Benjamin (@hextraza)
• Teresa Martinez (@teresam856)

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This discussion was created from the release Release v1.5.2.