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v1.6.5 Release

ยท 3 min read

We are pleased to announce v1.6.5!

This features some various bugfixes to the @jbrowse/cli tool, including better support for large config files with the admin-server, and renaming --out to --root for the admin-server.

It also includes two important fixes related to stats estimation in 1.6.4, one where tracks would display an error on sparse tracks and another where tracks would fail to perform stats estimation on BAM files due to a type confusion.

Downloadsโ€‹

To install JBrowse 2 for the web, you can download the link above, 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.

1.6.5 (2022-02-18)โ€‹

Packages in this release

PackageDownload
@jbrowse/corehttps://www.npmjs.com/package/@jbrowse/core
@jbrowse/plugin-alignmentshttps://www.npmjs.com/package/@jbrowse/plugin-alignments
@jbrowse/plugin-authentication
@jbrowse/plugin-bedhttps://www.npmjs.com/package/@jbrowse/plugin-bed
@jbrowse/plugin-dotplot-view
@jbrowse/plugin-hic
@jbrowse/plugin-legacy-jbrowsehttps://www.npmjs.com/package/@jbrowse/plugin-legacy-jbrowse
@jbrowse/plugin-linear-comparative-view
@jbrowse/plugin-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/plugin-linear-genome-view
@jbrowse/plugin-sequencehttps://www.npmjs.com/package/@jbrowse/plugin-sequence
@jbrowse/plugin-spreadsheet-view
@jbrowse/plugin-svghttps://www.npmjs.com/package/@jbrowse/plugin-svg
@jbrowse/plugin-variantshttps://www.npmjs.com/package/@jbrowse/plugin-variants
@jbrowse/plugin-wigglehttps://www.npmjs.com/package/@jbrowse/plugin-wiggle
@jbrowse/clihttps://www.npmjs.com/package/@jbrowse/cli
@jbrowse/desktop
@jbrowse/imghttps://www.npmjs.com/package/@jbrowse/img
@jbrowse/react-circular-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-circular-genome-view
@jbrowse/react-linear-genome-viewhttps://www.npmjs.com/package/@jbrowse/react-linear-genome-view
@jbrowse/web

๐Ÿš€ Enhancementโ€‹

๐Ÿ› Bug Fixโ€‹

  • Other
    • #2758 Use VariantTrack for plaintext VCF type (@cmdcolin)
    • #2738 Add better catch for XS and TS tag detection from CRAM (@cmdcolin)
    • #2733 Use sparse array for alignments coverage to fix bug viewing large sparse regions (@cmdcolin)
    • #2734 Use node fetch instead of follow-redirects in cli (@cmdcolin)
    • #2726 Handle .bgz file extension for text-index (@cmdcolin)
    • #2727 Add engines 16 to @jbrowse/img (@cmdcolin)
    • #2723 Make jbrowse desktop more robust to errors when reading recent sessions file (@cmdcolin)
    • #2715 Change --target to --root for jbrowse CLI admin-server (@cmdcolin)
  • core
    • #2757 Fix type confusion with stats estimation causing BAM files to fail byte size calculation (@cmdcolin)
    • #2750 Add bezierCurveTo to offscreen canvas ponyfill to fix sashimi arcs rendering in alignments track in webkit and firefox (@cmdcolin)
    • #2719 Avoid uninitialized state during stats estimation (@cmdcolin)
    • #2707 Fix ability to use authenticated assembly files (@garrettjstevens)
    • #2695 Fix disabled state on the linear genome view track labels dropdown menu (@cmdcolin)

๐Ÿ“ Documentationโ€‹

๐Ÿ  Internalโ€‹

Committers: 3โ€‹