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JBrowse 1.15.1

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@rbuels rbuels released this 02 Aug 00:23
· 875 commits to dev since this release

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, pull #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, pull #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,
    pull #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! (pull #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, pull #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, pull #1145, @cmdcolin)