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v1.6.8 Release

· 2 min read

We are pleased to announce the v1.6.8 release!

This release includes a change to the default gene style to use boxes instead of "chevron" features, with a directional arrowhead

Before

After

Some additional highlights

  • Draws the correct the proportion of SNPs when displaying the SNPCoverage height in log scale (thanks @gringer for reporting)
  • Adds more optimizations for some alignments tracks
  • Adds a per-base drawing mode to alignments tracks

Downloads​

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.

1.6.8 (2022-03-25)​

🚀 Enhancement​

🐛 Bug Fix​

  • Other
    • #2852 Fix misaligned features under breakpoint split view (@cmdcolin)
    • #2844 Fix layout of small features without labels for SvgFeatureRenderer (@cmdcolin)
    • #2839 Fix the drawing of SNP height when the SNPCoverage track is using log scale (@cmdcolin)
    • #2825 Fix tracklabels positioning not updating in UI after user selection (@cmdcolin)
  • core

Committers: 3​

v1.6.7 Release

· One min read

This release fixes an issue with JBrowse Desktop on v1.6.6 where the first tracks to be opened would not load.

It also adds a speed optimization for BAM files (in some cases, 5x speed improvement seen in deep coverage files), and fixes a scroll issue on wiggle tracks!

Downloads​

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.

1.6.7 (2022-03-16)​

🚀 Enhancement​

🐛 Bug Fix​

Committers: 2​

v1.6.6 Release

· 4 min read

We are pleased to release v1.6.6!

This contains several updated synteny features, including:

  • load .chain files from UCSC
  • load .delta files from mummer
  • load .anchors and .anchors.simple files from MCScan from the GUI
  • ability to "rectangularize" the dotplot view and improved dotplot view overviews (shows total bp of selected regions)

Screenshot showing updated import form with ability to load MCScan data

Screenshot showing multiple tracks open at once, with the .anchors (green, gene pairs) and .anchors.simple (black, larger synteny blocks) files from MCScan shown in the dotplot view

Note: MCScan functionality existed internally but was not easy to use. The configuration schema for MCScan anchors files changed also to load the .bed files at startup. See the config guide for details

We also have an updated configuration editor GUI with collapsible sections

Screenshot showing new collapsible (turquoise) sections in the config editor

A number of alignments track look and feel improvements were also added. The scale bar was made to just list the min and max values when the height is small, clip indicator position when horizontally flipped was fixed, and the headroom was removed making the snpcoverage take up the full height of the small area it uses.

There have also been some changes to how internet accounts work. If you use one of the built-in accounts like Google Drive or Dropbox, there's no need to change anything. If you've implemented your own internet account, though, see #2725 for more details.

Downloads​

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.

1.6.6 (2022-03-15)​

🚀 Enhancement​

  • core
    • #2796 Add collapsible accordion sections in configuration editor (@cmdcolin)
    • #2791 Add new coloring options for dotplot and ability to "rectangularize" dotplot view (@cmdcolin)
    • #2741 Allow ability to enter a space-separated locstring to open a list of regions (@cmdcolin)
    • #2725 Refactor InternetAccounts, add standard getFetcher (@garrettjstevens)
    • #2787 Display the total bp viewed in the header of the dotplot view (@cmdcolin)
    • #2767 Wiggle and SNPCoverage look and feel improvements (@cmdcolin)
    • #2746 Add .delta and .chain format adapters, fix ref name aliasing in synteny/dotplot views, and optimize very long CIGAR string in synteny view (@cmdcolin)
  • Other
    • #2799 Exit process after rendering to speed up jb2export (@cmdcolin)
    • #2793 Add abortcontroller polyfill to jbrowse-img to allow it to run under node 14 (@cmdcolin)
    • #2761 Add a --clean argument to jbrowse upgrade to clean up old files (@cmdcolin)
    • #2760 Make a configurable refNameColumn in RefNameAliasAdapter (@cmdcolin)

🐛 Bug Fix​

  • core
  • Other
    • #2797 Fix crash plotting methylation in sparse regions (@cmdcolin)
    • #2782 Fix display of cytobands when horizontally flipped (@cmdcolin)
    • #2678 Preserve double border line when using trackLabel offset and use smaller gap between snpcoverage and reads (@cmdcolin)
    • #2774 Fix overwriting broken symlink with --force in add-track CLI (@cmdcolin)
    • #2773 Fix using global stats autoscale on wiggle tracks (@cmdcolin)
    • #2766 Add a check for empty content blocks to fix rare empty stats estimation (@cmdcolin)

📝 Documentation​

🏠 Internal​

Committers: 2​

v1.6.5 Release

· 2 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.

Downloads​

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.

1.6.5 (2022-02-18)​

🚀 Enhancement​

🐛 Bug Fix​

  • 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)

📝 Documentation​

  • #2716 Update to node12 requirement for @jbrowse/cli (@cmdcolin)
  • #2605 Developer guide reorganization and create new API document (@cmdcolin)

🏠 Internal​

Committers: 3​

v1.6.4 Release

· 3 min read

This release has a couple long awaited features!

There are also some improvements to synteny and dotplot views. The synteny view can now render curvy lines and "square" the views (so they each have the same zoom level), and have individual search panels in the synteny view. You can now also vertically resize the linear synteny view panel allowing for a taller or shorter view! The rendering has also been sped up in both linear synteny and dotplot views with certain code paths being up to 40x faster.

Also check out the recording and notes from our PAG 2022 tutorial session!

Screenshot showing the new curvy lines of the synteny view with the grape vs peach demo http://jbrowse.org/code/jb2/v1.6.4/?config=test_data%2Fconfig_synteny_grape_peach.json&session=share-EdWfJj5aIY&password=S8PGj

note that 1.6.0-1.6.3 were slightly buggy and collected into 1.6.4 here

Downloads​

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.

🚀 Enhancement​

🐛 Bug Fix​

📝 Documentation​

  • #2663 Add documentation for URL params and session spec (@cmdcolin)
  • #2655 Add link to PAG 2022 youtube tutorial on demos page and course archive (@cmdcolin)

🏠 Internal​

  • core
    • #2649 Add Cypress test of package that uses embedded components (@garrettjstevens)
    • #2648 Avoid console.warns in tests due to writing to MST nodes that are not alive (@cmdcolin)
  • Other
    • #2657 Fix hot reload using yarn resolution on react-error-overlay (@cmdcolin)

Committers: 3​

v1.5.9 Release

· One min read

This fixes a babel misconfiguration in v1.5.8 that prevented embedded packages from working

Downloads​

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.

1.5.9 (2022-01-13)​

🐛 Bug Fix​

Committers: 1​

v1.5.8 Release

· One min read

This release fixes an important issue where @jbrowse/react-linear-genome-view and other embedded packages did not work with v1.5.5 due to a babel misconfiguration apologies to all affected!

Also we now can access the parent feature in jexl callbacks with parent(feature) or get(feature, 'parent') which is often needed when coloring subfeatures like exon/CDS features

This release also was made because v1.5.6 and v1.5.7 only were half-published to npm, so v1.5.8 fixes it here

Downloads​

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.

🚀 Enhancement​

  • core
    • #2629 Add ability to get parent feature in jexl syntax with either parent(feature) or get(feature,'parent') (@cmdcolin)
    • #2632 Add vertical resize handle to dotplot view (@cmdcolin)

Committers: 2​

v1.5.5 Release

· 2 min read

This release fixes an important bug for users of @jbrowse/react-linear-genome-view where some features would not be able to be clicked in v1.5.3 and v1.5.2.

It also adds some better layout in the feature details panel, improved typescript interfaces, and allows users to open multiple genome assemblies from the start screen in JBrowse Desktop

This release also supersedes v1.5.4 which failed to upload to npm properly

Downloads​

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.

🚀 Enhancement​

🐛 Bug Fix​

🏠 Internal​

Committers: 3​

v1.5.3 Release

· One min read

This release fixes @jbrowse/development-tools, which was broken in v1.5.2, and is otherwise identical to v1.5.2. See the v1.5.2 release announcement for details about that release.

Downloads​

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.

1.5.3 (2021-12-21)​

🐛 Bug Fix​

Committers: 1​

v1.5.2 Release

· 4 min read

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.

Example of new arc track

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!

Downloads​

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.

1.5.2 (2021-12-20)​

🚀 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
  • 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​

🏠 Internal​

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

Committers: 6​