IGV 2.18.4 - September 2024#

Bug fixes and other minor updates

• CRAM files would not load properly with genbank references using alternative chromosome names. Github issue #1573
• Genomes with "twobit" reference sequeneces triggered an error when reading near the end of the sequence. Github issue #1586
• Bigbed reading errors.

IGV 2.18.2 - August 2024#

Bug fixes and other minor updates

• Panning alignment track triggered re-ordering of alignment rows
• New options for read alignments marked 'duplicate'
  • Filter duplicates
  • Highlight duplicates with crosshatch pattern

IGV 2.18.1 - August 2024#

Bug fixes and other minor updates

• The command-line igvtools were not running correctly. GitHub issue #1540.
• Clicking on a feature track (e.g. the RefSeq track) in Collapsed mode would only display one feature. GitHub issue #1541.
• The curves representing splice junctions would sometimes “overshoot” the junction boundaries. GitHub issue #1535.
• Clarified the "zoom in" message for whole genome view. GitHub issue #1539.

IGV 2.18.0 - July 2024#

New features

• If a file does not have a recognizable filename extenstion, IGV now tries to determine the file format from the file contents. This works for BAM, CRAM, BigWig, BigBed, VCF, GFF3, and TDF content. GitHub issue #1526.
• New display mode for alignment tracks: Full displays a single alignment per row. GitHub issue #1531.
• New right-click menu option to remove empty data panels.

Bug fixes

• Wait cursor could hang in some situations.
• Chromosome order was not maintained when using FASTA files to define the reference genome. GitHub issue #1489.
• Now can automatically detect
• Restored missing BAM files to Encode 2012 menus.

Other updates

• Third Gen alignment preferences:
  • Quick consensus mode is now FALSE by default. GitHub issue #1516.
  • Hiding small indels is now FALSE by default.

• Long-read RNA-seq alignments are now assigned an experiment type of RNA by default. The experiment type can be changed to 3rd Gen via the track's right-click popup menu. GitHub issue #1491.

• Ultima Genomics alignment data. GitHub issue #1490.

  • Fixed several edge cases and inconsistencies in the coloring of data from Ultima Genomics.
  • Added a new option to the Alignment preferences: INDEL coloring uses min quality (ultima) colors indels by the minimal quality of the homopolymer run rather than by the quality of the specific change.
  • Thanks to Thomas Garrety (Hartwig Foundation) for insightful comments and feature suggestions.