Release v2.1.3

This release includes a quality-of-life improvement for users plotting synteny
with CIGAR strings. Before this version, the x-axis in the dotplot was assumed
to be target sequence (and similarly, the top row in the linear synteny view
was assumed to be the target sequence). But now, target can be either x- or
y-axis in dotplot, and top or bottom in linear synteny views, removing the need
for the user to care as much about query-vs-target ordering.

This release also includes several fixes for the the behavior of text searching
in the linear genome view, a new button to open a .jbrowse file directly from
the start screen on jbrowse-desktop, and an important bugfix to plotting
inverted alignments on dotplots that affected versions v2.1.0-v2.1.2.

Screenshot showing the latest jbrowse desktop start screen, with a button to open .jbrowse sessions

Screenshot showing both X/Y orientations of two yeast genomes on the dotplot view, focusing on the deletions and insertions.

Enjoy!

🚀 Enhancement

• Other
  • #3188 Add 'Open saved session' button to start screen on desktop (@cmdcolin)
  • #3187 Add mouseover tooltip descriptions to the header of the VariantFeatureDetails sample/genotype table (@cmdcolin)
  • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
  • #3178 Allow X/Y assemblies of dotplot or top/bottom selection of synteny views to be either query or target (@cmdcolin)
  • #3173 Add ability for CLI to recognize plaintext BED files (@cmdcolin)
  • #3162 Add about dialog with version number for embedded components (@cmdcolin)
  • #3163 Note for user to wait before re-launching app on desktop update (@cmdcolin)
• core
  • #3180 Improve adding assemblies internally, and use the assembly displayName in more places in the UI (@garrettjstevens)
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
  • #3175 Add OAuthModel InternetAccount token refresh (@andrzejgrzelak)

🐛 Bug Fix

• core
  • #3168 Fix search behavior when there are multiple matches in LGV header and when feature description matched in import form (@cmdcolin)
  • #3182 Fix "dead state tree node" error by creating snapshots of parent region for block calculations (@cmdcolin)
• Other
  • #3170 Fix drawing inverted CIGAR segments on dotplot (@cmdcolin)

📝 Documentation

• #3138 Documentation overhaul (@carolinebridge-oicr)

🏠 Internal

• Other
  • #3179 Add extendSession extension point to web and desktop (@garrettjstevens)
  • #3165 Use more defaults in rollup plugins (@garrettjstevens)
• core
  • #3183 Make pluginManager param to getFetcher optional (@garrettjstevens)
  • #3164 Typescript the QuickLRU module in @jbrowse/core (@cmdcolin)

Committers: 4

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin)
• Garrett Stevens (@garrettjstevens)
• @andrzejgrzelak