Release v2.8.0

[cmdcolin]

This release improves support for BEDPE and arc rendering of structural variants.

It also adds a new CLI command called jbrowse sort-gff that intends to help simplify the loading of GFF tabix tracks.

Usage:

jbrowse sort-gff yourfile.gff | bgzip > yourfile.sorted.gff.gz
tabix yourfile.sorted.gff.gz
jbrowse add-track yourfile.sorted.gff.gz --load copy --out /var/www/html/jbrowse2

The jbrowse CLI tool can load BEDPE files with simply jbrowse add-track yourfile.bedpe (or, optionally gzipped e.g. yourfile.bedpe.gz)

Screenshot showing the same data rendered as both a BEDPE file and VCF file with different variant types (<DUP>, <DEL>, <INV>, <TRA>). Notably, this arc rendering can render 'cross-region' or 'inter-chromosomal' arcs.

Also, if you haven't seen it, check out our new office hours and community call schedule! See https://jbrowse.org/jb2/blog/2023/11/03/office-hours/

🚀 Enhancement

• Other
  • #4045 Create multi-region arc display type for variant tracks (@cmdcolin)
  • #4050 Allow specifying alternative config.json path via global variable (@cmdcolin)
  • #4046 Show last autosave on jbrowse-web start screen (@cmdcolin)
  • #4044 Speed up "multi-region" navigation in search box (@cmdcolin)
  • #4032 Add jbrowse sort-gff subcommand (@cmdcolin)
• product-core
  • #4040 Strip baseUri in 'About track' copy config (@cmdcolin)
• core
  • #4035 Prompt to horizontally flip view when launching linear synteny view on inverted feature (@cmdcolin)
• app-core
  • #4024 Add right-handed arrow to view title to emphasize the focused view (@carolinebridge-oicr)

🐛 Bug Fix

• #4052 Fix browser back button behavior in jbrowse-web (@cmdcolin)
• #4043 Fix crash in "Open session" widget for sessions that have 'track-less views' (@cmdcolin)

📝 Documentation

• #4027 Add office hours and community meetings (@cmdcolin)

Committers: 2

• Caroline Bridge (@carolinebridge-oicr)
• Colin Diesh (@cmdcolin) Done in 2.23s.

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This discussion was created from the release Release v2.8.0.