JBrowse 1

JBrowse 1.9.1 maintenance release

April 25, 2013

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:

  • JBrowse-1.9.1.zip - 5.0M file SHA1 1dc089e42e626da5312a8091dbcd1972a1cfb0fd

  • JBrowse-1.9.1-dev.zip - 28.6M file SHA1 bc5bb43ad8b71a9190e8c2a400d7db2364882e09 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.

Recent Posts