New Jalview Patch Release: 2.11.1.1

Posted On: 
17-09-2020

We are pleased to announce that Jalview 2.11.1.1, the first patch release in the 2.11.1 series, is now available as an over the air update. You can also download standalone jars and the source for the new release via https://www.jalview.org/download

This patch release includes fixes for critical bugs, and also brings some new features suggested by the Jalview community.

  • Shift+arrow keys navigate to next gap or residue in cursor mode (enable with F2)
  • Support import of VCF 4.3 by updating HTSJDK from 2.12 to 2.23
  • Improved recognition of GZipped files from local disk or retrieved via the web
  • EMBL and EMBL CDS database records retrieved from the European Nucleotide Archive's Data API as 'EMBL Flatfile' records
  • Improved Java Console and logging to help track down problems
  • Improved support for Hi-DPI (4K) screens when running on Linux (Requires Java 11+)

Critical bug fixes include

  • Jalview runs correctly when launched with Turkish language settings
  • Peptide-to-CDS tracking broken when multiple EMBL gene products shown for a single contig (such as viral genomes)
  • Errors encountered when processing variants from VCF files yield "Error processing VCF: Format specifier '%s'" on the console
  • Count of features not shown can be wrong when there are both DNA and Protein features mapped to the position under the cursor
  • Sequence ID for reference sequence is clipped when Right align Sequence IDs enabled
  • Find doesn't report matches that span hidden gapped columns
  • Jalview ignores file format parameter specifying output format when exporting an alignment via the command line

See the full release notes at https://www.jalview.org/development/release-history/Jalview-21111