JBrowse 1

JBrowse 1.15.1 maintenance release

August 1, 2018

JBrowse 1.15.1 has been released!

Files for download

Minor Improvements

  • Add a internal code attribute for XHR requests that use byte-range headers so that if a server does not support it, an error is returned immediately. Thanks to @theChinster for the motivating example (issue #1131, issue #1132, issue #1134, @cmdcolin).

  • Speed up TwoBit file processing with a robust implementation of the file spec. The improvements are contained in a new npm module @gmod/twobit. Thanks to @cmdcolin for some testing and motivating examples. (issue #1116, issue #1146, @rbuels)

  • Added feature.get('seq') to CRAM features which enables detailed comparison of the read versus the reference with the renderAlignment configuration. (issue #1126, issue #1149, @rbuels)

  • Added support for 1000genomes CRAM 2.0 codecs via updates to the @gmod/cram npm module. (@rbuels)

  • Add some better formatting for rich metadata in the "About this track" dialog boxes for tracks. Thanks to Wojtek Bażant for the idea and implementation! (issue #1148, @wbazant)

Bug fixes

  • Fix bug where prepare-refseqs with indexed FASTA would allows scrolling past the end of the chromosome (@cmdcolin).

  • Fix long standing bug related to not being able to configure dataRoot in the config file. Now you can set dataRoot=mydirectory to make JBrowse load mydirectory instead of the default data by default (issue #627, issue #1144, @cmdcolin).

  • Added hashing of the BAM feature data to generate unique IDs in order to distinguish reads that have nearly identical information (same read name, start, end, seq, etc). If the reads literally have identical information in them JBrowse is still unable to display but this generally seems to be due to limited use case such as secondary alignments in RNA-seq (issue #1108, issue #1145, @cmdcolin)

Recent Posts