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@rbuels rbuels released this 13 Dec 18:05

Major improvements

  • Added ability to view paired read data as connected entities for BAM and
    CRAM store classes. There are multiple different viewing options for this
    including plotting by insert size, plotting as connected arcs, or pileup
    views for the paired reads. Additonally multiple color schemes are available
    for coloring by insert size, pair orientation, mapping quality, and more.
    Thanks to @garrettjstevens, @rbuels, @AndyMenzies, and @keiranmraine for
    testing. Also a big thanks to @jrobinso from @igvteam for contributions to
    CRAM code related to paired reads (pull #1235, @cmdcolin)

Minor improvements

  • For users with the "dev" or compiling JBrowse from source code, the ./setup.sh
    now performs a full webpack production build (pull #1223, @cmdcolin)

  • Created new BAM parsing mechanism using the npm module @gmod/bam.
    Users might see some modest performance improvements due to enhanced tooling.
    Thanks to @rbuels and others for testing and feedback (pull #1215, issue #1178,
    @cmdcolin)

  • setup.sh now supports setting a JBROWSE_PUBLIC_PATH environment variable for
    more flexibility in iframeless embedding scenarios (issue #1213, @rbuels)

  • Added support for indexing arbitrary fields from GFF3Tabix files by setting
    nameAttributes in the track config e.g. nameAttributes=name,id,customfield.
    (issue #1115, pull #1222, @cmdcolin)

  • Add support for generate-names to index VCF features that have multiple IDs in
    the ID column (@cmdcolin)

  • Added documentation on embedding JBrowse in an iframe and in a div, including
    how to embed JBrowse using a custom JavaScript object as a configuration
    (pull #1228, pull #1243, @rbuels and @garrettjstevens)

  • Added ability to render non-coding transcript types to the default Gene glyph
    which helps when a gene feature has a mix of coding and non-coding subfeatures
    (issue #1106, pull #1230, @cmdcolin)

  • Created new VCF parsing mechanism using the NPM module
    @gmod/vcf. Thanks to @cmdcolin and
    others for testing and feedback (pull #1227, issue #1199, @garrettjstevens)

  • Added ability to open "chrom.sizes" files from the Open sequence dialog
    (issue #1250, pull #1257, @cmdcolin)

  • Added a config datasetLinkToParentIframe to make the dataset selector use
    window.parent for when jbrowse is in an iframe (pull #1248, @enuggetry)

  • Improved error message that is displayed when a data file cannot be fetched
    via CORS (@rbuels)

  • Added some word wrapping for long unbroken fields in the View details
    popups. Thanks to @luke-c-sargent for the idea (issue #1246).

  • Added hideImproperPairs filter for Alignments2/SNPCoverage tracks which
    disambiguates from missing mate pairs (pull #1235, @cmdcolin)

  • Added useTS coloring option for RNA-seq strandedness, similar to the useXS
    that existed previously (pull #1235, @cmdcolin)

  • Added a --bgzip_fasta option for prepare-refseqs.pl and also the ability
    to index reference sequence names if they are manually specified as a
    fasta index e.g. refSeqs=genome.fai. Thanks to @FredericBGA for the report!
    (issue #1281, pull #1282, @cmdcolin).

Bug fixes

  • Fixed issue where some generate-names setups would fail to index features.
    Thanks to @BioInfoSuite for reporting (issue #1275, pull #1283, @cmdcolin)

  • Fixed issue with getting feature density from BAM files via the index stats
    estimation (issue #1233, @cmdcolin)

  • Fixed issue where some feature mouseovers where not working properly (issue
    #1236, @cmdcolin)

  • Fixed issue where instantiating JBrowse via standalone.js didn't work when
    in a production build with JBROWSE_PUBLIC_PATH overridden (issue #1239,
    @garrettjstevens)

  • Small fix for issue where SNPCoverage would crash on some feature filters
    (issue #1241, @cmdcolin)

  • Fixed issue where JBrowse Desktop was not able to access remote files (issue
    #1234, pull #1245, @cmdcolin)

  • Fix issue where the Hierarchical track selector contained a bunch of blank
    whitespace. Thanks to @nathanhaigh for reporting! (issue #1240, pull #1253,
    @cmdcolin)

  • Fixed issue where whitespace surrounding GFF3 attributes and attribute names
    was incorporated (issue #1221, pull #1254, @cmdcolin)

  • Fixed issue with some GFF3Tabix tracks having some inconsistent layout of
    features (issue #1244, pull #1260, @cmdcolin)

  • Fixed CRAM store not renaming reference sequences in the same way as other
    stores (pull #1277, @rbuels, @cmdcolin)

  • Fixed bug where older browsers e.g. IE11 were not being properly supported via
    babel (issue #1259, pull #1267, @cmdcolin)

  • Fixed bug where some files were not being fetched properly when changing
    refseqs. Thanks to @luke-c-sargent for the report (issue #1252)

  • Fixed storeTimeout on CRAM files being unused which can result in excessive
    fetches (pull #1235, @cmdcolin)

  • Fixed issue where JBrowse would load the wrong area of the refseq on startup
    resulting in bad layouts and excessive data fetches. Thanks to @hkmoon,
    @cmdcolin, and @garrettjstevens for debugging (issue #1190, pull #1235, pull
    #1187)

  • Fixed issue where CRAM layout and mouseover would be glitchy due to ID
    collisions on features (issue #1271, @cmdcolin)

  • Fixed parsing of certain bigBed files that were hanging on track startup
    (issue #1226, pull #1229, @cmdcolin)

  • Fixed issue where some parts of a CRAM file would not be displayed in JBrowse
    due to a CRAM index parsing issue (@cmdcolin)

  • Fixed an issue where BAM features were not lazily evaluating their tags
    (@cmdcolin)

Notable changes

  • Rendering of features in popups, mouseover tooltips, and feature labels were
    made to escape HTML. If you are using literal HTML labels in these places
    then set the attribute unsafePopup, unsafeMouseover, or unsafeHTMLFeatures
    on your tracks. Thanks to @garrettjstevens (pull #1263, @cmdcolin).