IGV 2.9.2 - Feb 2021#

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

IGV 2.9.1 - Feb 2021#

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

IGV 2.9.0 - Feb 2021#

New batch execution features:

• Major improvements to performance and stability of IGV batch execution.

• Respect maxPanelHeight when creating snapshots.

• 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): +, positive, -, negative
  • setShowSequenceTranslation - valid values (case insensitive): true, false

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 positive 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)