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IGV 2.13.x

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IGV 2.13.0, released May 2022

This release includes the following improvements and fixes:

  • Support for Amazon AWS default credentials. This enables loading data from AWS S3 using s3:// URLs if Amazon credentials can be found in the default credential chain as described in AWS documentation here. In addition, if default credentials are found, the default region chain will be searched as described in AWS documentation here. Cognito configuration, as described at https://umccr.org/blog/igv-amazon-frontend-setup/, will take precedence over default credentials.
  • Improved support for jumping to the next/previous feature in a selected feature track (using the "f" and "b" keys).
    • The feature is now centered in the view.
    • A preference can now be set to automatically zoom the view to fit the feature to the window, with optional up- and downstream padding. Go to the General tab in View > Preferences to set this preference.
    • A bug has been fixed where typing an "f" or "b" into text fields (e.g. the locus search box) was interepreted as a feature jump if a feature track was selected. (Git Issue #1122)
  • Support for handling a trailing "." or "?" character in the SAM tag MM (modified bases). (Git Issue #1131)
  • Support for GWAS files with "NA" in the p-value column, e.g. some files produced by new versions of PLINK. (Git Issue #1127)
  • When loading session files that included the showGenotypes property for a VCF track, the track would be displayed without the genotypes even when the property was set to "true". This has now been fixed.

IGV 2.13.1, released June 2022

This release includes the following improvements and fixes:

  • Major performance improvement for CRAM files (htsjdk 3.0).
  • CSI indexes can now be loaded from URLs (htsjdk 3.0).  (Git Issue #843) 
  • New menu item for feature tracks to specify the feature property to use for the displayed name.  (Git Issue #1089)
  • Improved support for BigBed files; extra fields are now included in the popup text.
  • Group-by-strand now works for feature tracks in collapsed mode.  (Git Issue #1151)
  • Prevent jumping beyond the end of the chromosome.  (Git Issue #1150)

IGV 2.13.2, released July 2022

This release fixes a problem with Sashimi plots - they were not displaying any splice junctions, only the annotation track.