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IGV 2.9.x

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IGV 2.9.0, released February 2021

This release includes the following new features and improvements:

New batch execution features

  • Major improvements to performance and stability of IGV batch execution.
  • New colorBy batch command to control coloring of alignments. Matches the menu in the alignment track.
  • New batch commands to control the sequence track. (Git issue #836, PR #868)
    • setSequenceStrand - valid values (case insensitive): +, postive, -, negative
    • setShowSequenceTranslation - valid values (case insensitive): true, false 
  • Respect maxPanelHeight when creating snapshots.

Other new features

  • New alignment track menu item to copy a clipped read sequence to the clipboard. (Git issue #860)
  • New option to group alignments by reference concordance. (Git issue #852)
  • Changing the track color for feature tracks now supports setting different colors for the postive and negative strands. 

Bug fixes

  • IGV would sometimes freeze when receiving commands from a port.
  • Bigbed tracks were not handling chromosome aliasing, causing the track not to load in some cases. For example, if chromosome 1 was specified as "1" in the file and as "chr1" in the reference genome.  (Git issue #898)
  • The name panel displayed extra characters for tracks loaded from URLs that had parameters with slashes ("/"). (Git issue #897)
  • Handle bed files with columns separated by multiple tabs (Git issue #890).  Bed files can be whitespace delimited, multiple consecutive tabs == a single "whitespace".
  • Tracks loaded from .narrowpeak files would sometimes be colored incorrectly, while tracks from .narrowPeak  (capital P) were correct. (Git issue 881)

 IGV 2.9.1, released February 2021

Fixes issue with federated Amazon S3 support. See GitHub pull request 904.  Contributed by @brainstorm at University of Melbourne Centre for Cancer Research (UMCCR).

 IGV 2.9.2, released February 2021

Fixes a bug where IGV eventually freezes with multiple error messages if you visit enough loacations in a BigWig track. This problem was introduced in IGV version 2.9.0.  (Git issue #911)