JBrowse 1

JBrowse-1.12.3: Maintenance Release

May 2, 2017

**We are happy to announce JBrowse 1.12.3 release! **

This release includes a lot of improvements and bugfixes and we thank the community for the support. Some great new features include parsers for new file formats including 2bit format, which can be loaded via prepare-refseqs.pl. There are also new parsers for tabix BED files, tabix GFF and IonTorrent BAM files. Some other improvements include a new noFill option to display BigWig tracks as a scatter plot, the cacheMismatches option that improves performance for BAM files with long reads, and many other small improvements and fixes.

In addition, visit the JBrowse Plugin Registry for a collection of great plugins.

Enjoy!

Minor improvements

  • Upgraded build system to install dependencies with bower and updated to dojo 1.9.8 (issue #718).
  • Added the ability to load tabix indexed GFF and BED files. Thanks to Colin Diesh and @zhjilin for contributing (issue #670).
  • Added ability to open BED files in the "Open track" user interface (issue #729).
  • Added ability to access SPARQL and other jbrowse data stores via CORS. Thanks to the WebApollo hackathon and Eric Rasche for contributing (issue #679).
  • Added extra coloring schemes for the Sequence track when using protein residues. Thanks to Eric Rasche for the idea and implementation (issue #673).
  • Added ability to specify custom exporter classes for the "Save track data" option, for example, adding exporter code in plugins (issue #682).
  • Added ability to specify custom name store classes via plugins, which allows plugins to implement their own search functionality (issue #732).
  • Added a timeout for the track feature density calculations which can aid problems like consistent chunkSizeLimit issues (issue #540, issue #730).
  • Added an option to specify multiple highlights, or bookmarks, using the config file, a remote service, or the URL bar (issue #668).
  • Added support for parsing BAM files from IonTorrent (issue #782, issue #568).
  • Added support for native file access to .2bit files (issue #759).
  • Added list of plugins in about box (issue #848).
  • Added cacheMismatches option to improve performance when viewing long-read alignments (issue #860).
  • Added subfeatureDetailLevel config item to make View details box only load subfeatures on demand (issue #861).
  • Added ability to draw scatter plot from BigWig tracks. Thanks to Keiran Raine for the contribution (issue #741).
  • Added a fullviewlink option for the URL bar to disable "View full link" attribute in embedded JBrowse. Thanks to Vivek Krishnakumar for contributing (issue #813).
  • Added URL parameter &tracklabels=0 and config parameter to hide track labels (issue #869).
  • Added renderAlignment option which creates a per-base alignment view of the read versus the reference (issue #795).
  • Added inferCdsParts option which creates CDS subfeatures from a continuous CDS region for CanvasFeatures glyphs. Thanks to Vivek Krishnakumar for the contribution (issue #872).
  • Added events tracks/focus, tracks/unfocus, allowing for context switching based on selected track.

Bug fixes

  • Made the menu bar widgets centered again (issue #680).
  • Fixed error where the sequence track would not load after "Open sequence file" (issue #831).
  • Fixed problem with persistant "Error reading from name store" message. Thanks to Anthony Bretaudeau for contributing the fix! (issue #820).
  • Reverted to standard eukaryotic codon set.
  • Fixed issue where saving session in JBrowse Desktop where plugins were not saved with session.
  • Fixed an error if there were numerical values being used as label or description for the CanvasFeatures type tracks. Thanks to Eric Rasche for reporting (issue #673).
  • Fixed some issues where the Gene glyph would not layout some features correctly. Thanks to Eric Rasche for reporting (issue #686).
  • Fixed an issue with JBrowse Desktop where saving session would not save the tracks that were not visible.
  • Added fix when using indexed fasta from prepare-refseqs.pl. Thanks to @billzt for the report (issue #719).
  • Added a fix for an issue where editing the configuration of files that were opened by a user didn't work. Thanks to @lpryszcz for the report (issue #569).
  • Fixed some inconsistencies where "Open sequence" on file with a .fasta file extension failed (issue #696).
  • Fixed issue where track labels would re-appear during scroll (issue #793).
  • Added handler for click scrolling in genome view. Thanks to @exogenesys for fixing (issue #709).
  • Fixed a rare error that only affected some versions of Chrome (issue #758).
  • Removed linear gradients from some NeatFeatures tracks (issue #721).
  • Fixed issue where saving GFF3 would fail if the source data was in VCF format (issue #800).
  • Fixed issue where there was a mix of plugin declarations (issue #866).
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