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IGV 2.14.0, released August 2022

New options for displaying sequence alignments:

• Color by base modification (5mC) specified with MM/ML tags in the BAM file. For more details, see https://github.com/igvteam/igv/wiki/5mC-coloring-mode.

• 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".