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@enuggetry enuggetry released this 04 May 01:21
· 2102 commits to master since this release
1.12.3-release
4849a83

Release 1.12.3 2017-05-02

Pre-Packaged downloads: http://jbrowse.org/jbrowse-1-12-3/

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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