IGV 2.7.x

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IGV 2.7.0, released October 2019

This release includes a number of new features and fixes:

  • Support for viewing data in Amazon S3 storage using native AWS authorization and authentication. Contributed by Roman Valls Guimera (@brainstorm), Florian Reisinger, and Oliver Hofmann from the University of Melbourne Center for Cancer Research (UMCCR), and Andrew Patterson from the Melbourne Genomics Health Alliance. See the UMCCR blog for details on using this feature.
  • Mutations in MUT and MAF files are now colored by mutation type by default. This can be disabled in the View Preferences > Mutations tab. The mutation colors can also be changed in the Mutations tab; note they are no longer in the View > Color Legends window. 
  • Viewing data via public Google URLs no longer requires a Google login.
  • The "useProxy" option is now ignored unless proxyHost is set. In previous versions of IGV, a null proxyHost would cause the application not to launch if "useProxy" was set.
  • Fixed an issue where index files were not always correctly recognized. For example, the file bamfile.bai was not always automatically loaded as the index file for bamfile.bam.
  • Fixed several issues related to sessions:
    • Sessions were not correctly handling relative file paths (Git issue #693). This was fixed, and sessions now use relative paths by default.
    • Group autoscale now works for overlaid tracks loaded from a session (Git issue #694)
    • The state of 'showDataRange' is now saved in session files  (Git issue #694)
  • Regions of interest were not displayed when imported from a BED file with chromosome names without the "chr" prefix. The import now uses the same chromosome aliasing as when the BED file is loaded as a track (Git issue #700)
  • Updated the windows installer to install desktop shortcuts for all users (Git issue #703)

IGV 2.7.1, released October 2019

  • Improvements related to the Amazon S3 support introduced in 2.7.0:
    • Improved performance for loading the AWS S3 data picker  (Git issue #705)
    • Improved user interface for AWS Glacier: Make sure the user is informed if a data object is Archived (Git issue #698)
  • Updated popup text for VCF tracks to recognize value for "missing" (Git issue #628)
  • Fixed several issues related to running batch scripts:
    • Incorrect placement of gene names in the annotation track in multi-locus view (Git issue #633)
    • Could not specify a genome in the batch script unless the ID was already in the genome dropdown menu
    • URL paths to genomes and FASTAs did not work with the "genome" command
    • Some preferences set in a batch script were ignored for 3rd gen and RNA alignment tracks (Git issue #640)

IGV 2.7.2, released October 2019

  • Increased scroll increment in the Preferences window  (Git issue #716)