CHANGES.txt

JBR Genome Browser Changelog
============================

Here you can see the full list of changes between each release.

Version 2.0.6853
----------------

Released on July 27, 2026

* Omnipeak support reworked to use the downloadable omnipeak.jar file
* Allow disabling separator between tracks via the "Show Separator" menu item
* Allow configuring the number of recent sessions via sessions.properties (https://github.com/JetBrains-Research/jbr/issues/301)
* Add View | Add separator menu item to insert a separator track with configurable color, title and height
* Fix "Save as PNG/SVG": show file chooser dialog, reveal a saved file in the file manager, correct retina display scaling (https://github.com/JetBrains-Research/jbr/issues/303)
* Allow BED-like tracks to use any column as the region label via the "Region Label Column" menu, applying changes immediately (https://github.com/JetBrains-Research/jbr/issues/295)
* Fixed the too many open BED files problem (https://github.com/JetBrains-Research/jbr/issues/309)
* When opening remote URL with an unknown extension, show a dialog to set in explictly (https://github.com/JetBrains-Research/jbr/issues/304)
* Configure memory settings within the User Interface
* Other bugfixes and minor improvements


Version 2.0.6785
----------------

Released on February 27, 2026

* Bug fix release
* Fixed the problem with missing genes in the track view due to caching problems
* Reworked the web server caching

Version 2.0.6765
----------------

Released on December 3, 2025

* Bug fix release
* Fixed IGV remote session loading
* Updated Omnipeak to 1.3.6762

Version 2.0.6746
----------------

Released on October 22, 2025

* Introduced Compact / Full mode settings - when titles and legends are shown over / above the track view
* Fixed Peak calling within the JBR
* Updated JVM runtime to 25 LTS

Version 2.0.6709
----------------

Released on August 8th, 2025

* Improved server mode memory management
* Bugfixes

Version 2.0.6694
----------------

Released on July 29th, 2025

* Support peak calling using BigWig files
* Bugfixes

Version 2.0.6685
----------------

Released on July 24th, 2025

* Support for [Omnipeak](https://github.com/JetBrains-Research/omnipeak) models.

Version 2.0.6643
----------------

Released on May 13, 2025

* Fixed semi-supervised SPAN model tuning, see https://github.com/JetBrains-Research/span/issues/45

Version 2.0.6642
----------------

Released on April 29, 2025

* Updated Java Runtime to Amazon Corretto 24
* Increased default memory settings to 8Gb
* Small UI fixes


Version 2.0.6600
----------------

Released on November 26, 2024

* BAM/SAM/CRAM files support
* Enhanced Bisulfite-Sequence DNA methylation BAM files visualization
* Enhanced actions history support including tracks modifications, navigations, etc.
* Select tracks by name or wildcard
* Detailed information of track data on mouse cursor hover
* Multiple panels support
* GTF file support
* SPAN 2.0 model support
* Enhanced memory management and optimizations due to Amazon-Corrette JDK 21 runtime
* Apple-silicon aarch64 support (M1+ CPU)


Version 1.0.5641
----------------

Released on March 13, 2023

* Create BigWig arithmetics track within the genome browser: sum, average, etc.
* Updated Docker image
* Bugfixes

Version 1.0.5577
----------------

Released on October 13, 2022

* Significantly faster web browser
* Enhanced large BED files rendering with advanced indexing
* Group scale mode for selected tracks
* Headless screenshots done from command line interface
* Support the latest SPAN release
* Advanced SPAN results visualization including underlying HMM model states
* Fixed web-based browser navigation when position is provided in URL
* Check for updates on startup
* Simplified web UI - removed logs view
* New version of bundled Amazon Corretto JRE
* Updated Docker image
* Bugfixes

Version 1.0.beta.5320
---------------------

Released on March 24, 2021

* Custom genome configuration editor
* Import and export of IGV sessions
* Import and export of UCSC sessions
* Improved searching and loading tracks from ENCODE portal
* Improved server mode memory consumption
* New version of bundled Amazon Corretto JRE
* Custom log file location support
* Docker image for easily setup a server
* Bugfixes

Version 1.0.beta.5198
---------------------

Released on Apr 22, 2020

* Latest SPAN 0.12.0.5096 support
* Support for searching and loading tracks from ENCODE portal
* Server mode visualizing single or multiple sessions in web browser
* Full support of High DPI displays
* Fixes

Version 1.0.beta.4882
---------------------

Released on May 17, 2019

* Latest SPAN 0.11.0.4882 support
* Now files without extension or with any extension could be opened as BED files (e.g. SICER files w/o extension)
* UI fixes (Genes track view blinking, Cytobands legend alignment, ..)
* Fixed executable flag for *.sh files in Linux distribution
* Support for any BED3+ files, BED file auto-format feature improved

Version 1.0.beta 2
------------------

Released on March 26, 2019

- Support all the chromosomes including contigs, random and alternative chromosomes
- Support screenshot in Scalable Vector Graphics format
- Support big fonts
- Built-in web server rendering improved
- BED files tuning capabilities by score field
- Improved about information in tabular format
- Fix startup on Linux
- Fixed antialiasing issues on Linux, Windows
- UI improvements
- Various other bugfixes


Version 1.0.beta 1
------------------

Initial release, released on Nov 22, 2018

- Integrated peaks annotating
- On-the-fly peak calling using SPAN models
- Support for observing multiple genome locations simultaneously
- Classical genome browser features to view various genome data formats
- Supported data file formats: BED (including MACS2, SICER peaks), WIG, TDF, BigBed, bigWig
- Supported sessions formats: JBR *.yaml, IGV *.xml session files
- Remote URL bigWig/BigBed/BED files support
- BED track peaks statistics
- BigWig signal statistics track for multiple locations
- Optimized for working with large sessions
- Built-in web server for session sharing