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JBrowse 1.15.4

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@rbuels rbuels released this 05 Oct 14:03
· 704 commits to master since this release
1.15.4-release
13b4941

Minor improvements

  • Added support for bgzipped indexed FASTA. To use, bgzip your FASTA with
    bgzip -i file.fa, which generates file.fa.gz and file.fa.gzi and then use
    samtools faidx file.fa.gz. If you specify the .fa.gz in the track config e.g.
    "urlTemplate": "file.fa.gz" and have all three files in your data directory,
    then they will automatically be detected (issue #1152, pull #1200, @cmdcolin)

  • Allow fna and mfa file extensions for FASTA to be recognized by default in
    the Open sequence dialog (issue #1205, @cmdcolin)

  • Improve the layout slightly for dense features (issue #1210, @cmdcolin)

  • Added a topLevelFeaturesPercent configuration variable that can be used to
    correct feature statistics estimates when topLevelFeatures is being used for
    a track, or when it contains deeply-nested features. This configuration variable
    is currently only used by BAM, BEDTabix, GFF3Tabix, and VCFTabix stores.
    (issue #1147, pull #1209, @rbuels)

  • Tabix-based data stores use a new storage backend based on the @gmod/tabix npm
    module. Users should see some modest performance improvements for Tabix-based
    tracks. (issue #1195, pull #1209, @rbuels)

  • Added hideSequenceBox config to allow hiding the FASTA boxes in the View details
    popups. Thanks to @andreamini for reporting (issue #1211, pull #1219, @cmdcolin)

  • Added categoryOrder config to allow sorting the categories in the Hierarchical
    track selector. For example, categoryOrder=VCF,Quantitative/Density,BAM. Note
    that we specify a lowest level subcategory e.g. Quantitative/Density to sort the
    parent category Quantitative to a position (issue #1203, pull #1208, @cmdcolin)

Bug fixes

  • Fixed a bug in which feature labels would sometimes be repeated across the view,
    in the wrong locations. (@rbuels)

  • Fixed error where a chunk size limit error during histogram display would not be
    displayed (@cmdcolin)

  • Fixed issue where Open sequence dialog will open up the default "data" directory
    instead of a blank instance (issue #1207, @cmdcolin)

  • Added check for PCR duplicates for CRAM features (@cmdcolin)

  • Fixed issue where editing the track names and types in the "Open track" dialog box
    was not working when editing multiple tracks (issue #1217, @cmdcolin)

  • Fixed issue in which large VCF headers were not always correctly parsed by JBrowse
    (issue #1139, pull #1209, @rbuels)

  • Fixed issue where the histogram Y-scale bar would appear over features (issue
    #1214, pull #1218, @cmdcolin)

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