2.4.0

March 2020

New Features

• New track type for splice junctions. See https://github.com/igvteam/igv.js/wiki/Splice-Junctions. Thanks to @bw2
• New color option for "no call" genotypes. See https://github.com/igvteam/igv.js/wiki/Variant-Track.

Bug Fixes

• Fix wig track rendering issue #1017 -- coverage gaps appear / disappear with zoom
• Improve handling of oAuth errors - more user feedback
• Fix popup text issue with collapsed VCF tracks #1060
• Correctly parse non-variant alleles (alt allele = ./.)
• Fix hardcoding of htsget endpoints #1061
• Always parse bam header for htsget read requests. Fixes #1062

2.3.5

November 2019

New Features

• "Whole genome view" is now optional. Use wholeGenomeView: false to disable it.
• File extension .regionPeak added as a synonym for .narrowPeak

Bug Fixes

• Bug fix - AED features with start position "0" were not parsed
• Bug fix - "sort by tag" initialization not working

2.3.3

New Features

• New Alignment track option to hide small indels, primarily for 3rd gen technologies (pacbio, nanopore, ...) with large numbers of spurious indels.
  • hideSmallIndels: true | false,
  • indelSizeThreshold: integer

Bug fixes

• Improved treatment of very deep coverage alignment files (>100,000x). Previous versions could freeze or crash the browser in some cases.
• SVG not saved in whole genome (all chromosomes) view.

2.3.2

Bug fixes

• TDF file loading error
• Sort-by tag not working for numeric tags

New features

• New alignment sort options
  • Sort by insert size
  • Sort by chromosome of mate

2.3.1

Minor bug fix release

• oauth not working for cram files
• html/css color names (.e.g "blue") failed in track configurations
• local files read in their their entirety, even if indexed

New sorting options for BAM tracks

• sort by tag
• sort by read strand

2.3.0

September 2019

This is a major release with respect to the code base. The most significant change is the conversion of all source files to ES6 modules. Additionally webpack has been replaced by rollup for building the distribution. There is one potentially breaking change to the API. The global "igv.browser" is no longer defined. If needed, you can define this global as follows

igv.createBrowser(div, options).
    then(function (browser) {
        igv.browser = browser;
   });

The most significant functional change is an optimization to reading BAM format files suggested by @adamkewley of PetaGene ltd. The optimization reduces the number of network requests significantly.

New features:

• BAM file load optimization.
• Support for GATK GCVF files with variants.
• New BAM alignment context menu item to view complete read sequence for an alignment.
• Track labels are now included with SVG output.

Bug fixes:

• Off-by-one bug for wig fixed-step and variable-step files
• .bgz extension not recognized

2.2.17-b2

September 2019
Minor patch fixing a bug affecting the gene search service for the igv web app.

2.2.17

Small release that fixes a bug that disabled "expand" mode for annotation tracks.

2.2.16

This release contains optimizations for large, non-indexed files.

• Display of whole genome view is now limited to tracks with < 100,000 features.
• Optimizations to support large wig tracks (> 10,000 features). Note bigwig format is still recommended.

New features:

• Add counts of deletions and insertions to coverage track popup.
• Add support for UCSC track line.

2.2.15

August 2019
This release has some minor enhancements and a significant optimization for deep coverage alignment tracks, and other tracks that have large numbers of rows. Canvas rendering is now limited to ~ 2x the vertical dimension currently in view, rather than the entire vertical dimension of the underlying track. As the view is scrolled vertically the backing canvas is re-rendered as needed.

• Limit vertical size of canvas to what's in view + 2x screen height.
• Increase default samplingDepth for BAM files to 1,000.
• Support for VCF "SV" variants.
• Display correct genomic positions in whole-genome view popup text.