IGV 2.14.x

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IGV 2.14.0, released August 2022

New options for displaying sequence alignments:

  • Shade by mapping quality. (Git Issue #1110)
  • Group by mapping quality. (Git Issue #1112)
  • Sort by aligned read length. (Git Issue #1159)
  • When grouping alignments by an attribute, the display order of the groups can now be reversed by selecting Group alignments by > Reverse group sorting in the right-click popup menu.  (Git Issue #1106)

Other updates and bug fixes:

  • The IGV application no longer checks to for new versions. (Git Issue #1117)
  • Bug fix: Combined data tracks could not be generated via Tools > Combine Tracks or restored from previously saved sessions.
  • Bug fix: Tracks generated via the BLAT and Motif finder tools were not being restored when a saved session file was loaded.
  • Bug fix: Sashimi plots displayed a maximum of one sample.
  • Bug fix: Saved .png images displayed a black background with black text for alignment track group labels. A white background is now used to match the onscreen appearance. (Git Issue #1172)
  • Bug fix: TDF files failed to load via URL when the URL had a query string. (Git Issue #1168)


IGV 2.14.1, released September 2022

Updates and bug fixes:

  • Improvements to alignment sorting.
  • New coloring option for alignments with base modification: "Color by base modification (all C)". Color Cytosine bases by most probable modification when specified by MM/ML tags.
  • Bug fix: Issues with alignment option "Color by base modification (5mC)" in the presence of "5hmC" modifications.
  • Bug fix: View as pairs broken if combined with "Color by ZMW".