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IGV 2.8.0, released January 2020

This release includes the following new features and improvements:

1. Sequence alignment tracks

• A number of default values are set based on the sequencing experiment type, which is inferred from the alignments when they are first loaded from the file, i.e., when the view is sufficiently zoomed in to a region that contains alignments. The alignment track popup menu now includes a new item where the experiment type can also be set explicitly. Values include: 'RNA', '3rd Gen', and 'Other' (the default). (Git issue #736). Note that any values that are set based on experiment type can be overriden in the preferences (View > Preferences).

• The Copy read sequence command in the track popup menu is now available when viewing alignments as pairs. (Git issue #580).

• BLAT searches can now be performed on soft-clipped sequences (if at least 20 bp in length). (Contributed pull request #728).

• Sorting alignments by start position now uses the first mapped base and ignores any soft-clipped bases. (Git issue #725).

• Fixed an issue with the read details presented in the popup text for read string = "*". The length was incorrectly presented as 1bp; it is now reported as "undefined". (Git issue #557).

• The Alignments tab of the Preferences window has a new option to specify the default display mode for alignment tracks. It can be set to EXPANDED, SQUISHED, or COLLAPSED. The display mode for an individual track can be changed via its popup menu. (Git issue #134).  

• The option to filter alignments by read group is back in the Alignments tab of the Preferences window. It had inadvertently been dropped in a previous release. 

2. Translation view in reference sequence track

• Coloring of start codons was previously based on the amino acid, not the codon. This meant that Methionine (M) was colored green whereever it was found, which is not always correct (e.g. for the Mitochondrial table). Now AUG/ATG are colored green. In addition, the genetic code tables can now include alternative start codons that are colored yellow. Specifically, for Vertebrate Mitochondria these are AUA, AUU, and AUC.  (Git issue #582). 

• In previous releases, the amino acids in view were not always updated when a different translational table was selected. This has now been fixed.

3. Sample attributes

• New feature: Overlay tracks based on a shared sample attribute via Tracks > Overlay. (Git issue #396).  

• New feature: Rename tracks based on a sample attribute via Tracks > Rename. (Git issue #681). 

• Renaming a track via the popup menu no longer disables its sample attributes. The attribute key is now the original track name, and so the track retains its sample attribute assignments when it is renamed. 

• Coverage and splice junction tracks for a .bam file are now assigned the same sample attribute information as the associated alignment track. (Git issue #524).  

• Reinstated the option to specify a sample attribute key to use for track names by default. This option was inadvertently dropped from the Tracks tab of the Preferences window in a previous release.

• Fix to allow the #sampleMapping section to stand alone in a separate text file. The behavior now matches the description in the user guide. (Git issue #523).  

4. Other new features and improvements

• Resize an existing Region of Interest by CTRL-clicking on its red region bar below the genome ruler and dragging to the new start or end position. (Contributed pull request #723)

• Change the view locus by dragging the red box in the cytoband view. (Git issue #674). 

• Add a new empty data panel to the display via View > Add New Panel. Move tracks into the panel by selecting the track names and dragging them to the new panel. (Git issue #258). 

• dbSNP searches are now supported for the following assemblies. Enter the SNP's RSID, e.g. rs172334, into the locus search box. (Git issue #477).
  • Human hg19 and hg38; dbSNP build 151 (source UCSC Browser)
    • Common SNPs, i.e. found in >= 1% samples
    • Flagged SNPs, i.e. rare, but flagged as clinically associative by dbSNP
  • Mouse mm10; dbSNP build 142 (source UCSC Browser)
    • Common SNPs, i.e. found in >= 1% samples

• New file type: Files of type regionPeak are now supported and are treated the same as narrowPeak files.

• New options when running IGV from the command line  (Git issue #611).
  • --help will print a list of available command-line options and then exit.
  • --version will print the IGV version and then exit.

• Fixed an issue with the display of read coverage in Sashimi plots. Sometimes the coverage seemed to disappear in zoomed out views. (Git issue #579). 

5. The menu that connected IGV to GenomeSpace has been removed. With the discontinuation of NHGRI funding for the GenomeSpace project its servers have now been shut down. See genomespace.org for more details.

 IGV 2.8.2, released March 2020

New features and bug fixes since the IGV 2.8.0 release include (note, there was no 2.8.1 release):

• New option to sort sequence alignments by 'read name' in the right-click popup menu.  (Git issue #419). 

• When loading a new sequence alignment track, the default is now to shade bases by quality. This preference can be changed in View > Preferences > Alignments. The min and max value thresholds for the shading can also be set in the preferences.

• When showing soft-clipped bases is enabled, you can scroll beyond the beginning/end of the reference sequence. Previously the max extension was hardcoded at 1000 bp; the exentension window size can now be set in View > Preferences > Alignments. (Git issue #783).

• Bug fix: Saved session files did not store the state of hidden junction tracks or the new name of renamed coverage tracks. This has now been fixed. (Git issue #766).

• Entering * in the locus search box will now display the whole-genome view. Other ways to accomplish the same thing include: entering All into the search box; selecting All from the chromosome dropdown menu; clicking on the 'whole genome view' icon in the toolbar. (Git issue #757).

• File > Reload Session now reloads the most recently opened or saved session file. (Git issue #659).

• Currently loaded tracks can now be reloaded from file by selecting File > Reload Tracks or by clicking on the 'refresh' icon in the toolbar. (Git issue #659).

• Bug fix: GWAS track names are now displayed correctly.

• Fix for Catalina MacOS: The igvtools file dialog has been updated to work with the restricted folders on Macs running Catalina.

 IGV 2.8.3, released May 2020

New features and bug fixes in the IGV 2.8.3 release include:

• R, G, and B color values can now also be specified as floating point values in the range 0.0-1.0. 

• Fixed null pointer exception that occurred when viewing BAM files without base qualities if a large visibility window was set. (Git issue #813).

• Fixed an issue where alignments were sometimes loaded even when the current region in view was larger than the visibility threshold window. (Git issue #804).

 IGV 2.8.4, released June 2020

New features and bug fixes in the IGV 2.8.4 release include:

• New performance improvements for loading alignments when multiple tracks share the same alignment data.

• Improvements to batch script execution to prevent the commands from getting out of sync. This should eliminate the need for inserting 'sleep' commands into the script to ensure that longer running commands complete before the next command in the script is executed.

• Fixed an issue with the 'Regions of Interest' tool. The mouse click that defines the first boundary of the region worked, but the second click was ineffective, and so the region was not created. (Git issue #799).

• Fixed issue with 'group base_at_pos' command in batch script execution. (Git issue #796).

 IGV 2.8.6, released June 2020

New features and bug fixes since the IGV 2.8.4 release include (note, there was no 2.8.5 release):

• By default, the popup information text is now displayed only when you click on a data element. Use the yellow balloon icon in the IGV toolbar to set the behavior to "hover", "click", or "none".

• All file dialogs now use the OS platform's native dialog. Previously, some dialogs used the Swing file dialog, which is not compatible with MacOS Catalina. One difference that users might notice is that when saving image files, there is no dropdown menu to select the image file type. Choose the image file format type by setting the name extenstion to .png, .jpeg, .jpg, or .svg when you save the file.

• Fixed an issue where the right-click track menu would not pop up in alignment tracks when alignments had previously been grouped by base at position.

 IGV 2.8.7, released July 2020

IGV version 2.8.7 fixes some issues related to the enhanced security of MacOS Catalina. In particular, it includes improvements related to accessing files in the restricted folders (Desktop, Downloads, Documents, and external and remote drives).

 IGV 2.8.9, released August 2020

New features and bug fixes since the IGV 2.8.7 release include (note, there was no 2.8.8 release):

• Fixed issue where selecting to view the mate of a paired-sequence alignment in split screen could cause IGV to hang.

• Updated the embedded Java to version 11.0.8.

 IGV 2.8.10, released October 2020

This release includes new download bundles for IGV. For the MacOS App and the Windows Installer, you can now choose to download a version with or without an embedded Java. If you prefer to use your own installation of Java 11, choose an IGV download that is labeled "Separate Java 11 required".

 IGV 2.8.13, released November 2020

• Fixed an issue where "View mate in split screen" was not working on systems localized to non-US regions.