JBrowse 1

JBrowse 1.10.3 maintenance release

September 4, 2013

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

Files for download:

  • JBrowse-1.10.3.zip - 4.8M file SHA1 3be482df63ce10a9211483bc760d3b4137a2e77f

  • JBrowse-1.10.3-dev.zip - 26M file SHA1 825093524bbf09f0f724f80332342b99f8e50734 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.
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