Release v2.18.0

[cmdcolin]

This release marks a number of improvements including

New multi-variant display modes

• Ability to display multi-sample VCF in a 'matrix' or 'stacked' style view
• Supports both large 1000 genomes style VCF or smaller trio VCF
• Allows users to cluster rows by genotype using a call out to R script

Screenshot of the multi-variant viewer

Major improvements to the spreadsheet and SV inspector views

• Allows opening tracks in the spreadsheet and SV inspector

• Uses @mui/x-data-grid for display of the spreadsheet

• Makes separate columns for VCF INFO fields

• Support larger files by storing data in 'volatile' storage that doesn't bog down the session

• Support DEL, INV, and all types of SVs instead of just TRA and BND type variants in the SV inspector

• Re-navigates existing breakpoint split view instead of launching a new one each time

screenshot showing the new datagrid for the SV inspector

screenshot showing that you can open up tracks in the import form of the SV inspector

Saves user sessions in a local IndexedDB

• Sessions are saved in IndexedDB instead of localStorage which has much higher capacity and organization, so you won't lose your sessions if your web browser closes!
• Users can create "favorite" sessions to revisit for later
• Admins can also create pre-configured sessions for their instancse for users

screenshot showing the new session manager with recent sessions, favorite sessions, and pre-configured sessions

Improved "aborting" behavior

This is an ongoing refactor, but there is now new improved 'aborting' behavior reducing some of the re-calculations that bog down the UI.

Optimized and improved jbrowse-plugin-gwas

• New optimizations added for loading large GWAS style BED datasets to enable better jbrowse-plugin-gwas features
• The jbrowse-plugin-gwas also added a better clickmap allowing you to see the mouse-over feature https://github.com/cmdcolin/jbrowse-plugin-gwas

2.18.0 (2024-12-10)

🚀 Enhancement

• core, product-core, sv-core
  • #4511 Add 'matrix' display for multi-sample VCFs (@cmdcolin)
• Other
  • #4692 Rename some session options on desktop "File" menu (@cmdcolin)
  • #4703 Add mobx transaction to multi-level synteny zoom (@cmdcolin)
  • #4696 BED optimizations for GWAS type data (@cmdcolin)
  • #4693 Add mate.name to LGVSyntenyDisplay feature mouseovers (@cmdcolin)
  • #4694 Allow opening bedpe files from users tracks in SV inspector (@cmdcolin)
  • #4672 Add BedGraphAdapter and BedGraphTabixAdapter (@cmdcolin)
• app-core, core, product-core, web-core
  • #4074 Autosave sessions in jbrowse-web IndexedDB database to make it easier to access old sessions (@cmdcolin)
• app-core, core, embedded-core, product-core, sv-core, text-indexing, web-core
  • #4682 SV inspector improvements (x-data-grid, opening track data, re-navigate breakpoint split view, support INV/DEL/more) (@cmdcolin)
• core, product-core
  • #4178 Add ability to use colorBy and filterBy for alignments track configs, and group by strand (@cmdcolin)
• core, product-core, text-indexing
  • #4663 Replace AbortSignal with "stop token" to rescue some aborting behavior (@cmdcolin)

🐛 Bug Fix

• #4708 Avoid full length sequence fetch on SNP coverage calculation (@cmdcolin)
• #4676 Fix MCScanAnchorsAdapter rendering in linear genome view (@cmdcolin)
• #4670 Fix GC-content track regression in v2.17.0 (@cmdcolin)
• #4667 Reduce self-pairing for some paired-end read data in breakpoint split view (@cmdcolin)

🏠 Internal

• __mocks__, app-core, core, embedded-core, product-core, sv-core, text-indexing, web-core
  • #4680 Add eslint-plugin-import for sort ordering (@cmdcolin)
• Other
  • #4675 Add fix for potential hydration mismatch errors (@cmdcolin)

Committers: 1

• Colin Diesh (@cmdcolin) Done in 1.52s.

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This discussion was created from the release Release v2.18.0.