Release v3.6.2

Hello all,

This release includes a relatively large refactoring of the CLI to use built-in node.js arg parsing, but other than that, these changes are just small bugfixes and usability improvements. Please see release notes for more info

3.6.2 (2025-07-10)

🚀 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 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)

📝 Documentation

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

🏠 Internal

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

Committers: 2

• Colin Diesh (@cmdcolin)
• Will Haese-Hill (@haessar)