IGV 2.6.x

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IGV 2.6.0, released July 2019

This release includes a number of new features and fixes:

  • GATK's MAFLITE mutation file format is now supported (Git issue #642).  
  • Popover text windows for mutations now include links to more information in CRAVAT at www.cravat.us. Enabled when viewing data with reference genome hg38.
  • Files in Dropbox can now be loaded into IGV. Use the File > Load from URL menu.
  • The level of transparency can now be adjusted in tracks that combine multiple overlaid tracks. Use the option provided in the track's popup menu (Git issue #480).
  • Tracks in the current IGV session can now be re-loaded using File > Reload Session. All the data tracks will be re-loaded, but the view and other settings remain the same (Git issue #659).  
  • The CTRL-F and CTRL-B feature for jumping to the next/previous variant site in a VCF track can now skip sites that are filtered out. If you select "Hide filtered sites" in the track's popup menu, any filtered sites will not be displayed and will not be included when jumping between sites. A checkmark will appear next to the menu item to let you know that those sites are not displayed in the track. Note that in previous versions of IGV, this menu item was named "Suppress filtered sites" and there was a bug that prevented jumping to the next/previous site if it was checked. (Git issue #638)  
  • Popover text when hovering over alignments in BAM tracks can now display CIGAR string lengths of up to 1000 (was 60)  (Git issue #667). 

IGV 2.6.1, released July 2019

  • Fixed bug where altColor specified in #track line was ignored by feature tracks.
  • Updates to new arcs support introduced in 2.6.0 (Git issue #631)
    • Accept "." as valid score in BEDPE files.
    • Support HICCUPS files. 

IGV 2.6.2, released August 2019

  • Fixed problem reading non-indexed annotation files by URL.

IGV 2.6.3, released August 2019

  • Fixed bug where a local FASTA file for a custome genome was also deleted from the file system when the genome was removed from the IGV dropmenu via Genomes > Remove Genomes (Git issue #675).
  • Fixed a problem that affected reading some gzipped files and produced the error message "Unable to create BasicFeatureReader using feature file, for input source <filename> ".