JBrowse 1.10.3 maintenance release

JBrowse 1.10.3 has been released, with a lot of small enhancements and important bugfixes.

Files for download:

Minor improvements

  • Added options to Alignments, Alignments2, and SNPCoverage tracks to
    allow hiding reads that are duplicates, fail vendor QC, have
    missing mate pairs, are secondary alignments, and/or are
    supplementary alignments. Thanks to Kieran Raine and Andrew Uzilov
    for pointing out the need for this, and for their input on its
    design (issue #332).
  • Added support for a variables configuration for SPARQL data
    stores that can be used to specify additional variables for
    interpolating into a SPARQL query. Thanks to Toshiaki Katayama for
    suggesting this.
  • Added the ability for Sequence tracks to display a 6- or 3-frame
    translation of the reference sequence. Thanks to Daniel Kasenberg
    for implementing this (issue #221).
  • Added checkboxes in the track menu of Sequence tracks that allow
    users to toggle the display of the forward strand, reverse strand,
    and 6-frame translation.
  • Added support for an addStores variable in the query string of the
    URL used to start JBrowse. This variable accepts store
    configurations (which are a way to specify data sources separately
    from track configurations, so multiple tracks can use the same data
    source) in JSON format. For example, to add a store called
    “urlbam” that points to a BAM file, you could use the JSON:{ "urlbam": { "type": "JBrowse/Store/SeqFeature/BAM", "urlTemplate": "/path/to/my/bamfile.bam" }}

    which, when URI-escaped and put in the query string, looks like:

    addStores=%7B%20%22urlbam%22%3A%20%7B%20%22type%22%3A%20%22JBrowse%2FStore%2FSeqFeature%2FBAM%22%2C%20%22urlTemplate%22%3A%20%22%2Fpath%2Fto%2Fmy%2Fbamfile.bam%22%20%7D%7D

  • Slightly improved performance of generate-names.pl in cases where
    –completionLimit is zero. Also improved the POD documentation of
    the –completionLimit parameter for generate-names.pl. Thanks to
    Richard Hayes for his continued patience.

Bug fixes

  • Fixed some bugs that prevented proper display of BigWig files
    larger than 4GB. Thanks to Keiran Raine for pointing this out.
  • Fixed a major performance bug that unnecessarily slowed down
    display of large BigWig files with Wiggle tracks when autoscale
    is set to “local”.
  • Fixed a bug that prevented display of BAM reads that had MD tags
    but no associated CIGAR string. Thanks to Keiran Raine for point
    this out (issue #330).
  • Fixed a bug in which FixedImage tracks (e.g. legacy image-based
    Wiggle tracks) never take down the “Loading” message when
    displaying on a reference sequence for which no image data has been
    provided.
  • Fixed a bug that prevented rendering of mismatches, insertions, and
    deletions in a BAM read that occurred after a skip. Thanks to Gregg
    Helt for noticing this and fixing it (issue #325).
  • Fixed a bug in which the SNP frequencies calculated by SNPCoverage
    tracks were sometimes incorrect. Thanks to Matthew Conte for
    pointing this out (issue #335).
  • Fixed a bug in which reference sequences with a start coordinate
    other than zero would cause the overview scale track to not be
    drawn correctly. Thanks to Gregg Helt for noticing this and
    working on an initial fix (issue #324).
  • Fixed a bug in which the most recent location visited on a given
    reference sequence was not properly being restored from the saved
    cookie. Thanks to Gregg Helt for the initial fix for this
    (issue #321).
  • Fixed a bug in which event handlers and blocks in CanvasFeatures
    tracks were not being properly cleaned up. The most prominent
    visible consequences of this were duplicate dialog boxes being
    opened when clicking on a canvas feature. Thanks to Keiran Raine
    for noticing this and making sure it was fixed (issue #329).
  • Fixed a bug with flatfile-to-json.pl parsing of GenBank locations.
    Thanks to Steve Marshall for pointing this out (issue #323).
  • Fixed a bug in which SNPCoverage tracks would not always properly
    display error messages when something goes wrong, particularly
    under IE 9.

About Robert Buels

JBrowse Lead Developer
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