IGV 2.3.x

IGV 2.3, released April 2013

New Features and Improvements

  • Motif finder. This new feature allows you to search for a particular nucleotide sequence in the reference genome, using either regular expression syntax or IUPAC ambiguity codes. Search results are displayed in two new tracks; one displays matches on the positive strand, and the other displays matches on the negative strand. Read more about it here.
  • Copy details of alignment coverage track to the clipboard. If you hover the mouse cursor over a sequence alignment coverage track, the pop-up window shows details about the reads at that locus, including the number of reads, and the distribution of called nucleotides. You can now copy this information to your computer's clipboard by right-clicking and selecting Copy Details to Clipboard from the menu.
  • Improved memory performance for BAM files. In this release, sequence alignments that are no longer in view are purged from memory more frequently than before. "Out of memory" messages should happen less often.
  • Gitools integration. Gitools is a framework, developed at the Biomedical Research Park in Barcelona (PRBB), for analysis and visualization of genomic data. Data and results are represented as browsable heatmaps. Data can be exported from IGV in gitools format, or loaded directly into a running gitools session. Available under the Tools menu. See http://www.gitools.org for details. 
Bug Fixes
  • Improved parsing of GFF3 files, so alternate coding sequences are displayed properly.
  • Fixed loading of BAM files over FTP.
  • Fixed bug where "Load Genome" dialog was sometimes blank.
  • Set autoscale to false when scale manually set, don't disable "Set Data Range" when autoscale set.
  • Trim any leading bases from VCF files which match the reference, so variants are displayed where the variation actually starts.

IGV 2.3.2  April 22, 2013

Bug Fixes
  • Cannot load large tdf or tabix files over http from some servers.

IGV 2.3.3  May 1, 2013

Bug Fixes
  • Minimum junction setting is ignored in splice junction track.
  • "Goto mate region" jumps to whole chromosome view when mate is on another chromosome.

IGV 2.3.4  May 13, 2013

Bug Fixes
  • File handes for "tribble" indexed files are not being closed.
  • Dragging in split screen / gene list view is broken.
  • Coverage track height cannot be changed.

IGV 2.3.6  May  2013

Bug Fixes
  • Null pointer exception creating snapshots from batch script.

IGV 2.3.7  May 30, 2013

  • The region-of-interest (ROI) batch command now takes an optional "name" argument.
Bug Fixes
  • When viewing VCF files with large numbers of samples view is not refreshed after scrolling vertically.
  • IGV fails on startup with Java 8

IGV 2.3.8  May 31, 2013

Bug Fixes
  • Fails to use proxy settings when performing byte range requests.
  • Searching for full chromosome causes no view change if already zoomed in

IGV 2.3.10  July 7, 2013

New features and Improvements
  • Display message when BEDTools plugin encounters an error
  • Show genomic location in tooltip of alignment tracks
  • Sashimi plot for RNA-Seq alignments
  • Option to override user preferences via a batch comman>
  • Option to direct igvtools output to stdout for count and sort commands, using the special string 'stdout' as the output file.
Bug Fixes
  • igvtools outputs incorrect wig files (multiple track lines)
  • SVG files are not readable by some programs (e.g. gimp) on Windows platform due to incorrect encoding.

IGV 2.3.12  July 15, 2013

Bug Fixes
  • Some bigwig files fail to load with a "null pointer exception"

IGV 2.3.13 August 2, 2013

  • Pickup default  proxy settings from environment variables.
Bug Fixes
  • UTRs not recognized in GFF files

IGV 2.3.14 August 6, 2013

  • Implement autoscale for splice junction tracks
Bug Fixes
  • Loading bedgraph files fail with "array index out of bounds" error

IGV 2.3.15 August 19, 2013

Bug Fixes
  • Show read sequence of unmapped mates 
  • Exons not associated with transcripts in GTF files
  • Splice junction tooltip incomplete in collapsed mode

 

IGV 2.3.16 August 20, 2013

  • Add "export consensus sequence" option to alignment track menu

IGV 2.3.17 August 26, 2013

  • Disable native Mac dialog when IGV is launched from Java Web Start 

IGV 2.3.18 September 5, 2013

Bug Fixes

  • Autoscale option is reset after navigating to new locus
  • Reference sequence track is not shown from session files if there is no assoicated annotation track

IGV 2.3.19 September 27, 2013

Bug Fixes

  • Popup messages appear when running batch scripts from the command line
  • Starting from the command line with a session file fails if no genome was previously selected
  • IGV hangs when viewing soft-clipped alignments at coordinates < 0  (5' end of contig)
  • Not all exons are displayed from Wormbase GFF files

IGV 2.3.23 October 24, 2013

New Features and Improvements

  • Add preference to control display of default sample/track attributes
  • Performance improvements for loading BAM files over the web
  • Development version only: Remove tracks via delete or backspace key
  • Allow multiple motifs to be entered at once in MotifFinder
  • Allow grouping of VCF tracks

Bug Fixes

  • Starting igv with the -g option causes a null pointer exception when genome is in current directory
  • Cannot read BAM files when server doesn't return Content-Length
  • Cannot read eQTL files with missing q-value

IGV 2.3.26 January 17, 2014

New Features and Improvements

  • Add option to overlay data tracks
  • A new option for loading files from the ENCODE project has been added to the file menu for genome assemblies hg19, b37, and mm9.
  • Provide 1-click download of genome and sequence files. 
  • Add additional options for loading files by URL, can specify the index file and TDF file location with "index" and "coverage" query parameters respectively.
  • Allow EPS snapshot output, through use of EPSGraphics library. See https://www.broadinstitute.org/software/igv/third_party_tools#epsgraphics for instructions
  • Add "remove" batch command, syntax "remove <trackName>"
  • Add 'ctrl-s' hotkey for sorting alignments by most recent sort
  • Read pairs are now downsampled together (both kept or both removed)

Bug Fixes

  • Fallback from HEAD to GET for HTTP requests if HEAD fails. Useful for loading from cloud providers such as AWS
  • When long error messages are displayed, they are scrollable