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[Snyk] Upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.4 #381

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[Snyk] Upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.4 #381

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@jonkiky jonkiky commented Oct 29, 2024

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Snyk has created this PR to upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.4.

ℹ️ Keep your dependencies up-to-date. This makes it easier to fix existing vulnerabilities and to more quickly identify and fix newly disclosed vulnerabilities when they affect your project.

  • The recommended version is 12 versions ahead of your current version.

  • The recommended version was released on a month ago.

Release notes
Package name: @jbrowse/react-linear-genome-view
  • 2.15.4 - 2024-09-20

    Fixes Hi-C files failing to load in v2.15.3 and also fixes text indexing on JBrowse Desktop on Windows machines

    2.15.4 (2024-09-20)

    🐛 Bug Fix

    Committers: 1

  • 2.15.3 - 2024-09-19

    This release (hopefully) fixes the SSL code signing on the Windows version of the jbrowse desktop app. This should help auto-updates work better on Windows

    2.15.2 (2024-09-18)

    🚀 Enhancement

    🐛 Bug Fix

    🏠 Internal

    • #4569 Refactor GFF3 parser to avoid returning internal _linehash variable (@ cmdcolin)

    Committers: 1

  • 2.15.2 - 2024-09-18

    v2.15.2

  • 2.15.1 - 2024-09-12

    This release adds a bugfix for slow loading times due to a refname aliases bug

    It also adds a new visualization mode for breakpoint split view to show paired read and split read orientations, helping to show things like inversions

    image

    🚀 Enhancement

    • core, sv-core
      • #4561 Create notion of launching a single-row breakpoint split view (@ cmdcolin)
    • Other
    • core
      • #4554 Fix the ability to sort menu items by priority for CascadingMenu (@ cmdcolin)

    🐛 Bug Fix

    • Other
    • core
      • #4553 Fix performance regression since v2.14.0 in assembly loading (@ cmdcolin)

    🏠 Internal

    Committers: 1

  • 2.15.0 - 2024-09-04

    This release has a couple updates

    • Update to MUIv6
    • Fix bug with BigBed names processing
    • Fix bug with e.g. @ jbrowse/react-linear-genome-view's view menu appearing incorrectly

    🚀 Enhancement

    • app-core, core, embedded-core, product-core, text-indexing, web-core

    🐛 Bug Fix

    • core, embedded-core
      • #4544 Fix cascading sub menus bug in embedded components in v2.14.0 (@ cmdcolin)
    • core
    • app-core

    Committers: 1

  • 2.14.0 - 2024-08-28

    This release adds some significant new features

    • Alignments track 'Group by' functionality: this features allows you to split an alignments track by a specific tag such as RG or HP into multiple new session tracks
    • A new adapter type to display sequence names from NCBI FASTA file such as NC_000001.10 in the user interface as chr1. This specifically targets the NCBI "sequence_report.tsv" format to do this renaming, and is called NcbiSequenceReportAliasAdapter

    image

    Example screenshot after applying the new Alignments track "Group by" functionality to group by the HP (haplotype) tag. Note that technically, each group is launched as a separate new "session track"

    🚀 Enhancement

    • core
      • #4532 De-duplicate snackbar messages (@ cmdcolin)
      • #4516 Add NCBI sequence_report.tsv alias adapter, with ability to recode NCBI fasta files to use UCSC style names (@ cmdcolin)
    • Other
      • #4533 Allow setting sequenceType='pep' in ReferenceSequenceTrack configuration (@ cmdcolin)
      • #4531 Add UnindexedFastaAdapter for fetching small plaintext FASTA files (@ cmdcolin)
      • #4528 Add description config slot to reference sequence track (@ cmdcolin)
    • app-core, core
    • core, product-core

    🐛 Bug Fix

    🏠 Internal

    • Other
      • #4530 Consolidate gff3 adapter featureData routine, avoid Number-ifying null phase (@ cmdcolin)
    • core
      • #4518 Don't send displayModel to "rendering" components on server side (@ cmdcolin)
    • __mocks__, app-core, core, embedded-core, product-core, text-indexing, web-core
      • #4513 Add new eslint rules (no-unnecessary-condition, no-unused-expressions, etc) and tsconfig noUncheckedIndexedAccess (@ cmdcolin)
    • app-core, core, embedded-core, product-core, text-indexing, web-core
    • core, product-core, text-indexing

    Committers: 2

  • 2.13.1 - 2024-07-31

    Fixes bug that caused the track selector in the linear synteny view to be unable to open in v2.13.0

    Also allows users to hide the track "outlines" in the linear genome view as an aesthetic preference

    without track outlines

    image

    with track outlines, and menu item to toggle it

    image

    🚀 Enhancement

    🐛 Bug Fix

    • #4501 Fix opening track selector in linear synteny view causing crash in v2.13.0 (@ cmdcolin)
    • #4495 Fix log scale for some types of signal tracks (@ cmdcolin)

    Committers: 1

  • 2.13.0 - 2024-07-25

    This release adds the ability to see the assembly name on each row of the synteny view, and adds a number of other small fixes

    image

    Example screenshot showing the assembly names on the far left for each row of a synteny view

    🚀 Enhancement

    🐛 Bug Fix

    • core
      • #4483 Fix configuration settings for track sorting in the track selector (@ cmdcolin)
    • Other
      • #4476 Fix config editor crash in vite usage of embedded components in dev mode (@ cmdcolin)
      • #4473 Fix 'Show no tracks active button' checkbox not working (@ cmdcolin)

    📝 Documentation

    🏠 Internal

    Committers: 3

  • 2.12.3 - 2024-06-27

    This is a hotfix release for a bug in desktop that affected v2.12.2 that prevented sessions from being started

    🚀 Enhancement

    • #4465 Add contig to the default dontRedispatch list for Gff3TabixAdapter (@ cmdcolin)
    • #4464 Bump generic-filehandle to put URL in error messages (@ cmdcolin)

    🐛 Bug Fix

    📝 Documentation

    • #4466 Add demo of using farm-fe bundler for embedded components (@ cmdcolin)

    Committers: 1

  • 2.12.2 - 2024-06-21

    This was a hotfix release to the v2.12.0 release to fix a Buffer is not defined error. See v2.12.0 release notes for more features https://github.com/GMOD/jbrowse-components/releases/v2.12.0

  • 2.12.1 - 2024-06-21
  • 2.12.0 - 2024-06-20
  • 2.11.2 - 2024-06-03
from @jbrowse/react-linear-genome-view GitHub release notes

Important

  • Check the changes in this PR to ensure they won't cause issues with your project.
  • This PR was automatically created by Snyk using the credentials of a real user.

Note: You are seeing this because you or someone else with access to this repository has authorized Snyk to open upgrade PRs.

For more information:

@snyk-bot
fix: upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.4
05c0c97 
Snyk has created this PR to upgrade @jbrowse/react-linear-genome-view from 2.11.2 to 2.15.4.

See this package in npm:
@jbrowse/react-linear-genome-view

See this project in Snyk:
https://app.snyk.io/org/jonkiky/project/24b00042-56a8-40ef-ab6f-11e5db23e008?utm_source=github&utm_medium=referral&page=upgrade-pr
@sgvallala sgvallala closed this Oct 29, 2024
@sgvallala sgvallala deleted the snyk-upgrade-719ea671b6ab9f8f1983d19daa026728 branch October 29, 2024 19:31
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@jonkiky @sgvallala @snyk-bot