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IGV 1.5.x

IGV 1.5.64 released April 2011

  • Change to "whole genome" view.   Chromosomes occupying less than 1 pixel in width are no longer drawn in this view. 

IGV 1.5.63, igvtools 1.14 released April 2011

  • Bug Fix: IGVTools failed when creating files > 2GB in size

IGV 1.5.59 released March 2011

  • Improvements to down-sampling algorithm used to limit coverage depth.
    • Filtering reads before the specified depth is achieved is now much less likely.
    • Less memory is needed for deep coverage files.

IGV 1.5.57 released March 2011

  • Bug Fix: Hard clip followed by a soft clip not handled properly in SAM cigar strings.
  • Bug Fix:  The coverage track occasionally incorrectly shows "zero" coverage for a locus.

IGV 1.5.52 released February 2011

  • Bug Fix: Memory leak with BAM files.

IGV 1.5.51 released February 2011

  • Bug Fix: Track line parsing error for "maxHeightPixels" parameter.

IGV 1.5.50 released January 2011

  • Updated Picard jar to resolve incompatibility with current samtools release.

IGV 1.5.49, released January 2011

  • Bug Fix: Loading a GFF file fails if the annotation column equals "."

IGV 1.5.48, released January 2011

  • Bug Fix: IGV fails to startup if cached .genome files are corrupt.

IGV 1.5.44, released December 2010

  • Bug Fix: Attributes (column 9) from GTF files were not displayed in popup text.
  • Bug Fix: Images saved as .jpeg and .png files have color errors.  Specifically, the RGB values were shifted slightly.  If the color was very close to grey this could cause, for example,  very light red to become very light blue.
  • New alignment color options:  Color by read group and sample
  • Exon sequence:  When selecting "Copy Sequence" from the popup menu over an exon, the sequence of the region spanning the exon is now copied rather than the entire transcript or gene.

IGV 1.5.43, released December 2010

  • Chromosome alias definitions.  Aliases to and from UCSC conventions  (e.g 1 -> chr1 and chr1 -> 1) are now automatically generated.

IGV 1.5.37, released November 2010

  • Bug Fix:  Multiple bugs were fixed with read alignment selection.
  • New maximum depth setting for alignment tracks.  IGV now limits the maximum depth displayed as individual alignments.  All alignments are still used for the coverage track count,  but if necessary they are down-sampled to the maximum depth setting for display.  This results in a significant reduction in memory required for deep-coverage regions.  For example, chrM of the CEU Daughter alignment file can now be loaded in ~150 MB,  previously it took almost 10 GB to load the entire region.  The default setting is 100x, and can be set on the Alignments tab of the user preferences window  (first screenshot below).  The setting for an individual track can be changed dynamically by right-clicking over the alignments and setting the depth (second screenshot below).

             

 

            

IGV 1.5.35, released November 2010

The following optional command line arguments have been added

  • -b <batchFile>  Immediately run the supplied batch script after start up
  • -g <genomeId> Specify the genome.   Example:  java -Xmx750m -jar igv.jar -g hg18

IGV 1.5.34, released October 2010

  • Bug fix:  A fix for a Vista bug inadvertently changed the location of the "igv" folder on Windows computers.  Instead of the <user home> (e.g. C:/Documents and Settings/<user name>)  the folder was moved to  "My Documents".  This has been corrected.   The consequence of this bug is that imported genomes might disappear from the menu.  
  • Bug fix:  The "expand" and "collapse" batch script commands failed if no track name was provided.
  • Bug fix:  Loading of .cn files failed if the file included blank cells.

IGV 1.5.33, released October 2010

  • Bug fix:  Probes in .gct and .tab files could not be mapped to the genome based on loaded annotations.  This is now fixed.  If an otherwise unmapped probe identifier is found in a loaded annotation track the coordinates of the annotation are used to map the corresponding expression value to the genome.
  • Bug fix:  The locus parameter in session files was ignored.

IGV 1.5.30, released October 2010

  • Relative file paths can now be used in session XML files.  If the "relativePath" attribute of a Resource element is set to true the resource file path will be interpreted relative to the location of the session file.  Note: if relativePath is used the corresponding "Track" elements, if any, for the file will be ignored. 
  • IGVTools "count" command will now output a .wig file in addition to or instead of a .tdf file.  Use ".wig" as the output file extension.  To output a .tdf and .wig file list both output files as a single string, separated by a comma with no delimiters.  This change is also included in the separate igvtools download, version 1.5.10.
  • Bug fix:  Due to a bug in the Java release for Windows Vista and Windows 7, IGV would occasionally fail to start due to a file permissions error when creating or writing to the "igv" folder.  In this release a warning and option to specify the location of the "igv" folder is given.

IGV 1.5.27, released October 2010

  • Ascii alignment formats (SAM, .ALIGNED) are now loadable over http.  These formats must still be indexed.
  • The UCSC "YC" tag is now supported for specifying alignment color in BAM files.  For more details see http://genome.ucsc.edu/goldenPath/help/hgBamTrackHelp.html.
  • The estimate of "feature visibility window" for indexed feature files has been adjusted.  The previous estimate was too conservative, resulting in very small window sizes before features were loaded.   Note that you can always override this value by right-clicking or by specifying it on a track line.
  • Bug fix: Region list is truncated in session files

IGV 1.5.25, released September 2010

  • Bug fix: Proxy username not saved after editing in the preferences window.

IGV 1.5.24, released September 2010

  • DAS 
    • A validity check that caused many Ensemble sources to fail with the message "No DAS capabilities found" has been removed.  
    • The "type" parameter is now supported.  This parameter is required for the UCSC data server, without it the entire database for an assembly is returned.  
    • The full URL to the feature source is now required.  Previously the "/features" command was added to the end of the URL if missing. 
    • A "feature visibility window" of 250 kb is now set for DAS tracks.  Zooming out past this window will result in no features being shown.  The window size can be changed by right-clicking on the track.  To disable windowing, resulting in whole-chromosome queries,  set the window size to zero.

See http://www.broadinstitute.org/igv/LoadData for more details.

  • Chromosome Alias Table.   IGV now supports user-defined aliases for chromosome names.  The alias table can allow data and alignments to be loaded that follow a naming convention that differs from the IGV genome, for example  "1" vs "chr1".  The table is defined by creating a tab delimited file with 2 columns,  column 1 contains the alias, column 2 the equivalent chromosome name in the IGV genome definition (for example, chr1.fa <tab> chr1).  The file must be named <genome id>_alias.tab and placed in the following directory:
    • <user home>/igv/genomes, or
    • <user home>/.igv/genomes if you have a Mac

IGV 1.5.21, released September 2010

  • Bug fix: Alignments loaded from .sam files could "disappear" after zooming out and back in.
  • The track line can now be used with .seg files.  The line must start with #track.

IGV 1.5.20, released September 2010

  • Alignment viewing improvements
    • Reads can now be highlighted by entering a read name via the popup menu.  Reads matching this name will be highlighted with a colored border.  The option does not search for reads, merely highlights them if in view.
    • Soft clipped bases can now be optionally displayed.  This is off by default, and can be set on the Alignments tab of the preferences window.  When "show soft clipped bases" is on dragging past the edges of the chromosome/contig is enabled.
    • Reads that are marked "vendor failed" are now filtered by default.  This is set on the Alignments tab of the preferences window.
  • New options for Regions of Interest
    • A region can be given a short description or name. 
    • Zooming to a region
    • A new sort option for copy number data, Sort by breakpoint amplitudes, had been added.  This option sorts copy # tracks by the sum of the absolute value of copy number changes within the region.
    • Keyboard shortcut - ctrl-R to define a region of interest for the region currently in view.
  • Data server improvements
    • A UCSC track line can now be set with a trackLine attribute in the XML file.  When set, this takes precedence over the track line defined in the file, if any.
    • A sampleID attribute for use with a sample info file can now be explicitly set on the resource element in the XML file.
    • File URLs can now be specified in the resource element in the XML files.
    • The "data registry URL" can now refer to a password-protected file.
  • Feature track improvements
    • The "expand/collapse" triangular icon on feature tracks is now optional.  The option is controlled from the "Tracks" tab of the preferences window.
    • The visibility window setting for feature tracks is now specified in units of kilo-bases, rather than bases
    • If available, feature density will now be displayed automatically as a heatmap in a feature track when zoomed out beyond the visibility window.  To enable this, the density must first be computed with the igvtools "count" command.  The resulting tdf file must follow the naming convention <feature track filename>.tdf.
  • Miscellaneous
    • New zoom option - click and drag in genome ruler panel below the cytoband.
    • You can now load URLs with "drag and drop".  Loading files with "drag and drop" was already supported.
    • Navigation history is now tracked.  You can view and select loci visited from the "View > Go to" menu, and navigate back and forward with alt-arrow.

igvtools 1.5.9, released September 2010

  • Bug fix: Sorting resulted in insertion of extra tab character at the end of lines.
  • Bug fix:  Records from variable step wig files were truncated by 1 base when converting to TDF format

IGV 1.5.18, released August 2010

  • Bug fix: Memory for loaded bam files was not released when a new session was created.
  • Bug fix: Regions-of-interest from separate chromosomes could get interchanged during display, leading to erratic results when sorting by score.
  • Bug fix: IGVTools sort command failed when using the -m option.
  • A warning is now displayed when attempting to load un-indexed ASCII format files exceeding 50MB in size.  It is suggested the such files be indexed or converted to the binary .tdf format prior to loading. 

IGV 1.5.17, released August 2010

  • Bug fix: In some cases a sample-info file could be mistakenly loaded as a bed track.
  • Bug fix: The igvtools "count" and "tile" command fails if the output "tdf" extension is not provided.
  • Bug fix: A significant performance bug was fixed affecting preprocessing of GCT files with the igvtools "tile" command. 
  • The UCSC .psl format is now supported.  This includes igvtools support for sorting, indexing, and computing coverage with the "count" command.  PSL files must end with the extension ".psl".
  • A new menu item, "Copy Details to Clipboard", has been added to the feature track popup menu.  This action will copy the popup text for the selected feature to the clipboard.

IGV 1.5.16, released August 2010

  • Bug fix: Setting track name from a sample info attribute was not working.
  • Bug fix: Loading an un-indexed vcf files failed without warning. 
  • Bug fix: Loading BAM files over HTTPS  (as opposed to HTTP) failed

IGV 1.5.13, released July 2010

  • Bug fix: Tabix indexed bed files will not load if track line is present
  • Bug fix: IGV sometimes hangs while initializing genome on startup
  • Bug fix: VCF files would not load if quality was set to "."

IGV 1.5.11, released July 2010

  • Bug fix: BedGraph data extended to the right by one base.
  • Bug fix: Track lines in genome annotation ("import genome") files were ignored
  • Bug fix: GFF parser bug -- GFF3 annotation lines with no ID field were ignored.  This caused display problems with the TAIR9 annotations, among others. 

  • New track line extensions (see http://www.broadinstitute.org/igv/TrackLine for details)
    • specify a log scale for charts
    • specify a "feature visibility window" for indexed feature tracks
  • You can now specify a track line in a server xml resource element.  If set, this value will override the track line, if any, in the file.  Example:

        <Resource name="adipose"
                  trackLine="track viewLimits=0:1000 scaleType=log"
                  path="http://www.broadinstitute.org/igvdata/BodyMap/Coverage/HBM.adipose.bam.sorted.bam.tdf"/>

IGV 1.5.08, released July 2010

  • Bug fix: Rows in .wig files with "*" for chromosome name are now ignored, rather than throwing an error.
  • Bug fix: Proxy username is now correctly saved.
  • Bug fix: A bug in the alignment indexer that caused alignments at the beginning of a SAM file to be ignored is now fixed.  Alignment index files created with version 1.5 to 1.5.07 should be deleted and recreated.

IGV 1.5

released June 30, 2010

New File Menu Options

Distributed Annotation Server (DAS) support. There is now an option under the File menu to load features from a DAS server.  This option is experimental and subject to the following limitations:

  • The segment parameter is ignored; features will be loaded per chromosome on demand.
  • No validation is done of the DAS source with respect to the currently selected genome.   

An example DAS URL, valid for hg18 and b36, is: http://das.ensembl.org/das/ens_36_omim_genes.

Batch Execution. There is now an option under the File menu for users who want to execute a series of sequential tasks: File>Run Batch Script.  Users can load a .txt file that contains a list of commands, one per line, that will be run by IGV. The accepted commands are the same as the IGV Port Commands as seen here: http://www.broadinstitute.org/igv/batch.

New Preferences Options

Change to Treatment of Segmented Copy Number files. Space between adjacent copy number segments now appears gray by default.  To enable the joining of adjacent copy number segments, select View>Preferences>General tab and select the checkbox for Join Adjacent CopyNumber Segments.

Coverage (.tdf) Track Normalization. There is a new option to normalized coverage tracks computed with igv tools.  This normalization option multiplies each value by [1,000,000 / (totalReadCount)].  Enable this option by selecting View>Preferences>Tracks tab and selecting the Normalize Coverage Data checkbox.

This is only available for .tdf files created using igvtools builds dated 1/28/2010 or later.  Previous versions of igvtools did not record the total read count.

Dynamic Autoscale. By default, charts (barchart, scatterplot, and lineplot)  now automatically adjust the plot Y scale to the data range currently in view.  As the user pans and moves, this scaling will continually adjust.  To turn autoscaling off by default  select View>Preferences>Charts tab and uncheck the option. This option can also be set for a single track from the popup menu.

Allele Frequency Threshold. Users can now set the mismatch threshold at which bases on an alignment coverage track are colored.  To change the default threshold, select View>Preferences>Alignments tab. The default of 0.2 can be changed in the Coverage allele-freq threshold field.  The threshold for an individual track can be changed from the popup menu.

Proxy Settings. Proxy settings are now supported for accessing the IGV genome and data server from behind a firewall.  Specify the proxy setting by selecting View>Preferences>Proxy tab.  

Other Improvements

Postscript output replaced by SVG. The postscript (.eps) output option has been replaced with scalable vector graphics (.svg). 

Improvements to Sessions. Many bugs related to restoring sessions have been fixed.   The changes should be backward compatible with 1.4.2 sessions. 

Genome Import. When genomes are imported from a single FASTA file, the order of the sequences within the FASTA are maintained in the Chromosome drop-down list. 

Password-protected Files. Basic authentication is now supported for files loaded by HTTP.  For information on how to set up an Apache server directory to be password protected, see this page. 

BED File Support. The UCSC track line options itemRGB, useScore, and url are now supported.

Heatmaps. Heatmap scale settings can be set per track.

New File Formats

  • MAF files are supported for mutations.  The file extension must be ".maf".

  • Birdseed files are supported for copy number.  The file extension must be ".birdseye_canary_calls".

Arguments for Command Line Startup. Users who start IGV from the command line can now specify a single session file or a comma-delimited list of files (as the first argument in the command), and can add a locus string or gene to zoom to as a second, optional argument.  

Exporting Selected Nucleotide Sequences. Users can now copy the sequence of a feature or region to the clipboard.  To copy the sequence of a feature, right-click on the feature and select Copy Sequence.  To copy the sequence of a region:

  1. Click the Define a region of interest icon in the tool bar.

  2. Click the red bar above the data panel and below the chromosome map that represents the region.

  3. Select Copy Sequence in the popup menu.

Indexed BED and VCF files. Large BED and VCF version 3.2 files can now be indexed with IGVTools (1.5)  or tabix.