You're Invited:Meet the Socket Team at BlackHat and DEF CON in Las Vegas, Aug 4-6.RSVP
Socket
Book a DemoInstallSign in
Socket

@jbrowse/plugin-menus

Package Overview
Dependencies
Maintainers
6
Versions
48
Alerts
File Explorer

Advanced tools

Socket logo

Install Socket

Detect and block malicious and high-risk dependencies

Install

@jbrowse/plugin-menus - npm Package Versions

2345

3.6.3

Diff
c
cmdcolin
published 3.6.3 •
c
cmdcolin
published 3.6.2 •
c
cmdcolin
published 3.6.1 •
c
cmdcolin
published 3.6.0 •

Changelog

Source

3.6.0 (2025-07-10)

:rocket: Enhancement

  • Other
    • #5102 Refactor CLI to use built-in nodejs parseArgs (@cmdcolin)
    • #5090 Optimize some MM tag parsing for performance and readability (@cmdcolin)
    • #5087 Better usage of dark mode on sequence track (@cmdcolin)
  • core
    • #5095 Fix alpha rendering of SVG renderer box stroke/fill (@cmdcolin)
    • #5086 Add status message reporting for synteny view loading (@cmdcolin)

:bug: Bug Fix

  • Other
    • #5100 Fix adding .pif file from dotplot and linear synteny import form (@cmdcolin)
    • #5098 Also migrate the linear-comparative-view rubberband tooltip to default MUI tooltip to avoid potential UI hangs (@cmdcolin)
    • #5097 Fix make pif on large files throwing ENOBUFS error in certain cases (@cmdcolin)
    • #5089 Additional type check to catch non-string MM tags from older Cell Ranger version BAM files (@haessar)
    • #5085 Fix rubberband getting stuck under certain conditions (@cmdcolin)
    • #5080 Fix crash on multi-wiggle importer on jbrowse-web (@cmdcolin)
  • core
    • #5095 Fix alpha rendering of SVG renderer box stroke/fill (@cmdcolin)

:memo: Documentation

  • #5099 Update readme with short description of what JBrowse 2 is, new links, and publications (@cmdcolin)

:house: Internal

  • __mocks__, app-core, core
    • #5077 Bump generic-filehandle with mock for test environment (@cmdcolin)

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.5.1

c
cmdcolin
published 3.5.1 •

Changelog

Source

3.5.1 (2025-06-05)

:rocket: Enhancement

  • Other
    • #5064 Optimize fetching many small sequences from IndexedFasta (e.g. MSA datasets) (@cmdcolin)
    • #5059 Canonicalize refNames in search results (@cmdcolin)
    • #5056 Use assembly displayName on synteny header and ruler (@garrettjstevens)
    • #5050 Use standard sessionId for linear synteny view to reduce data re-fetching (@cmdcolin)
  • app-core, core, embedded-core
    • #5063 Improve usability of dropdown menus by making submenus not disappear immediately onMouseLeave (@cmdcolin)
  • core
  • app-core, core
    • #5044 Allow plugins to register entries onto the root configuration (@cmdcolin)

:bug: Bug Fix

:memo: Documentation

:house: Internal

  • Other
  • core
    • #5061 Modularize some integration tests for launching views (@cmdcolin)

Committers: 2

yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.5.0

c
cmdcolin
published 3.5.0 •

Changelog

Source

3.5.0 (2025-05-27)

:rocket: Enhancement

  • #5042 Avoid inferring CDS subfeatures from non-coding gene pred features (@cmdcolin)
  • #5035 Use trash icon for uninstall in plugin store, and add version number string (@cmdcolin)
  • #4735 Remove jbrowse-web start screen (@cmdcolin)
  • #5025 Allow hiding insertion and deletion in synteny view to help chain file visualization (@cmdcolin)

:bug: Bug Fix

  • Other
    • #5037 Check that breakpoint split view is ready before fetching to avoid crash/large data fetching (@cmdcolin)
    • #5033 Bump @gmod/bbi to fix loading bigwig files from bigtools (@cmdcolin)
    • #5024 Fix lines crossing over view headers in breakpoint split view by only setting sticky view headers on top-level views (@cmdcolin)
  • core

:house: Internal

  • core
  • Other
    • #5036 Remove the async keyword from BaseLinearDisplayModel (@cmdcolin)

Committers: 2

yarn run v1.22.18 $ lerna-changelog --silent --silent --next-version 3.4.0

c
cmdcolin
published 3.4.0 •

Changelog

Source

3.4.0 (2025-05-13)

:rocket: Enhancement

  • core
    • #5018 Avoid serializing large features to sessions to fix quota exceeded errors in localstorage (@cmdcolin)
    • #5010 Add mouseover metadata for fields in the base feature widget (@cmdcolin)
    • #4998 Add padding to the genomic window of search result hits (@cmdcolin)
    • #4995 Add uFuzzy to improve gene name search (@cmdcolin)
    • #4983 Update some data parser packages for ESM compat (@cmdcolin)
    • #4980 Synthesize displayId if none provided in display config (@cmdcolin)
    • #4972 Support cytoband bed files starting with "#" (@cmdcolin)
  • Other
    • #5008 Allow parsing non-indexed BED files larger than 512MB (@cmdcolin)
    • #4997 Better message for "quota exceeded" message from localstorage (@cmdcolin)
    • #4974 Minor optimizations in multi-sample variant rendering (@cmdcolin)
    • #4973 Add basic cytoband for Drosophila (@cmdcolin)
    • #4970 Dynamically toggle wheel-scroll normalization to improve touchpad pinch-to-zoom usage (@cmdcolin)

:bug: Bug Fix

  • core
    • #5013 Fix UCSC chain parsing which have header lines (@cmdcolin)
    • #4993 Fix re-export of @mui/material/styles, and re-export theme (@cmdcolin)
    • #4968 Fix theme augmentation for primary/secondary colors in v3.3.0 (@cmdcolin)
  • Other
    • #5004 Fix modifications rendering broken in v3.2.0 (@cmdcolin)
    • #4992 Fix mouseover for some variable width bigwig features (@cmdcolin)
    • #4984 Avoid rendering 'yellow' for low scores in wiggle density renderings with 'log-scale' enabled (@cmdcolin)
    • #4969 Avoid aggregating bigbed features with geneName === 'none' (@cmdcolin)

:memo: Documentation

:house: Internal

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.3.0

c
cmdcolin
published 3.3.0 •

Changelog

Source

3.3.0 (2025-04-18)

:rocket: Enhancement

  • core
    • #4956 Add simplified display of REF/ALT to help with long strings produced by e.g. Cactus VCF (@cmdcolin)
    • #4954 Add genotype frequency table to variant feature details (@cmdcolin)
    • #4952 Add 'genotype' column to the Variant sample grid (@cmdcolin)
    • #4944 Show ALT allele description on multi-variant mouseover (@cmdcolin)
    • #4922 Add Multi-variant SV display (@cmdcolin)
  • Other
    • #4950 Add ability to use jexl filters on multi-sample variant displays (@cmdcolin)
    • #4934 Add alpha-transparency to help show overlapping SVs in the Multi-sample variant display (@cmdcolin)
    • #4931 Show target zoom level in tooltip on slider (@cmdcolin)
    • #4930 Upload last release build to https://jbrowse.org/code/jb2/latest (@cmdcolin)
  • app-core, core, embedded-core, product-core, sv-core, web-core

:bug: Bug Fix

  • Other
    • #4929 Fix broken bigbed features when there is gene level aggregation (@cmdcolin)
  • core

:memo: Documentation

  • core
    • #4949 Controlling navigation of embedded component - storybook examples (@cmdcolin)
    • #4924 Add config docs for pre-processors with simplified config snapshots (@cmdcolin)
  • Other

:house: Internal

  • core

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.2.0

c
cmdcolin
published 3.2.0 •

Changelog

Source

3.2.0 (2025-03-22)

:rocket: Enhancement

  • core
    • #4919 Add in-app clustering method for multi-wiggle tracks (@cmdcolin)
    • #4909 Add ability to load refNameAliases from chromAliases.bb file (@cmdcolin)
    • #4906 Add in-app clustering method for genotype matrix (@cmdcolin)
  • Other
    • #4914 Allow looking up header column by name for RefNameAliases (@cmdcolin)
    • #4910 Allow refNameColumn in RefNameAliasAdapter to override the default displayed refnames (@cmdcolin)
    • #4907 Simplified snapshot API for initial navigation of LGV (@cmdcolin)
  • app-core, core, product-core, web-core
    • #4899 Add aborting to multi-variant rendering, multi-wiggle rendering (@cmdcolin)

:bug: Bug Fix

  • #4920 Fix issue where multi-level linear synteny view would show a blank tracklist (@cmdcolin)
  • #4913 Fix parent aggregation in BigBed files using larger request window (@cmdcolin)
  • #4905 Fix bug where applying genotype clustering twice produces randomness (@cmdcolin)
  • #4897 Fix clustering for certain sets of bigwig files (@cmdcolin)

Committers: 1

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.1.0

c
cmdcolin
published 3.1.0 •

Changelog

Source

3.1.0 (2025-03-14)

:rocket: Enhancement

  • Other
    • #4876 Allow inferring default values of adapter urls to simplify config.json (@cmdcolin)
    • #4875 Add sample data from HGSVCv3 to 1000 genomes demo and config_demo (@cmdcolin)
    • #4880 Allow selecting track error messages with click and drag (@cmdcolin)
    • #4882 Allow clustering multi-wiggle tracks on the fly (@cmdcolin)
    • #4874 Use a '012' matrix to improve clustering of genotypes (@cmdcolin)
  • core
    • #4871 Add deletion, insertion, skip, softclip, hardclip to theme (@cmdcolin)
  • app-core, core, product-core

:bug: Bug Fix

Committers: 2

yarn run v1.22.22 $ lerna-changelog --silent --silent --next-version 3.0.5