JBrowse 1.9.1 maintenance release

JBrowse 1.9.1 has been released, with performance improvements in both BAM and VCF tracks, and lots of smaller fixes and improvements.

Files for download:

Changes in this release:

  • Significant speed and memory optimizations in BAM data backend
    (issue #242).
  • Significant speed and memory optimizations in VCF data backend.
  • JBrowse now attempts to smooth over mismatches in the naming of
    reference sequences between various datasets. For instance, if a
    BAM file contains reference sequences named like “chrom1”, and the
    canonical reference sequences used in a JBrowse installation are
    named like “chr1”, JBrowse will recognize these two names as
    equivalent for the purposes of displaying the BAM data. This
    behavior can be disabled by setting the global configuration
    variable exactReferenceSequenceNames to true. (issue #239).
  • Removed support for track blockDisplayTimeout configuration
    variable. It never worked very well, and the problem it was meant
    to address (delays caused by large data) are better mitigated by
    maxHeight and the faster rendering offered by canvas-based track
    types.
  • Fixed a bug that prevented displaying some VCF files. Thanks to
    Steffi Geisen for pointing this out.
  • Reduced the default value of maxHeight for canvas-based feature
    tracks (like Alignments2) from 1000 to 600.
  • Fixed a bug in the Alignments track type where BAM features with
    missing mate pairs that are not drawn due to their position above
    the track’s maxHeight caused the track rendering to crash.
    Thanks to Tristan Lubinski for reporting this.
  • If no global refSeqOrder is specified in the configuration, the
    reference sequences are now not sorted. Currently, this means that
    they will appear in the same order as loaded by
    prepare-refseqs.pl. Users with a very large number of (more than
    10,000) reference sequences may wish to avoid specifying a
    refSeqOrder, since sorting the reference sequences is done at
    JBrowse startup time. Thanks to Tristan Lubinski for reporting
    this.
  • Fixed bug preventing display of quantitative data from files loaded
    with flatfile-to-json.pl. Thanks to Gwendoline Andres for pointing
    this out.
  • Instead of quantitative (wiggle) tracks throwing an error when they
    cannot choose a min and max for the display scale, they now just
    make a guess. While probably wrong, this at least has the track
    displaying something, and users can then look up how to fix the
    display scale.
  • Added support for a chunkSizeLimit configuration variable for BAM
    and VCF-based tracks, which defaults to 5MB for BAM and 15MB for
    VCF. When fetching data, if a given region requires fetching a
    file chunk that is larger than this limit, a ‘Too much data’
    message is displayed. This helps prevent speed and memory problems
    when displaying deep-coverage BAM tracks and large VCF tracks
    (issue #242). Thanks to Gustavo Cerquiera (GitHub user cerca11)
    for pushing for progress on this.
  • Fixed a regression in which callbacks and interpolations were not
    evaluated in left-click and right-click menu configurations.
  • Fixed incorrect display of negative values in log-scale wiggle
    tracks. Thanks to GitHub user drusch for pointing this out
    (issue #244).
  • Fixed more minor errors when running under IE 7.
  • Fixed “Max height reached” message sometimes being drawn under
    instead of over HTML-based features.

About Robert Buels

JBrowse Lead Developer
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