Versions

Here is a list of the older versions of GenPlay that you can download.

It is important to know which version a project of GenPlay was saved with (in case there is a problem of compatibility with a newer version).

If you start GenPlay from the WebStart, which we recommend since it is a simple way to control the amount of memory assigned by the system to GenPlay, you might have to empty your browser cache to be able to start the latest version of GenPlay. Google "empty cache" and the name of your favorite browser to find instructions on how to empty your cache. The GenPlay version number is indicated on the upper-left corner of the title bar of the main  GenPlay application window.

GenPlay v996
Release date: 01-09-2014

Download: jar file

- Correction of a bug in the thread pool that made GenPlay slower after running for an extended period of time.

- Bugs on score repartition for bin list corrected.

- Various bug corrections and improvements.

GenPlay v978
Release date: 10-15-2013

Download: jar file

- Bugs on gene layer / extract exons operation corrected

- Bugs on gene layer / extract intervals operation corrected

GenPlay v976
Release date: 09-24-2013

Download: jar file

- Multi-genome bugs corrected

- OSX integration improved

GenPlay v972
Release date: 09-10-2013

Download: jar file

New operation for Methyl-Seq analysis: generate CG methylation profile

A new operation on sequencing tracks to combine the score on the C base with the score on the G base of a CG sub-sequence has been added.

GenPlay v970
Release date: 08-09-2013

Download: jar file

GenPlay

Track Layers

- Genomic data files are now loaded as layers instead of tracks.

- Tracks can can contain multiple layers.

- Layer options (color, graph type, visible) are available in the Track Setting menu item of the track contextual menu.

- Operation menus are now associated to layers instead of tracks.

Data structure

- Memory usage greatly improved for all layer types.

- The fix window, variable window and mask layers have been partially merged. Operations tend to be more similar between these types of layers and the creation of these layers can be done through a single consolidated interface available from the track contextual menu in "Add Layer" -> "Sequencing / Microarray Layer".

File Loading

- File extraction and data structure construction is now done in one step (instead of two) and loading is considerably faster than in the previous versions. Peaks of memory consumption have been greatly reduced.

- Sequence layers are faster to load.

Assemblies

- Rat genome rn5 has been added

GenPlay v584
Release date: 05-17-2012

Download: jar file

GenPlay

Warnings report - Previously name "Errors Report".

- Display priority between the "Warnings Report" dialog and other dialogs improved.

- New kind of warning: type of treatment "has been skipped"/"position has been shrinked to fit the chromosome length".

Two Track Operation

- Operation improved for variable windows tracks.

- Result track improved. In some cases, the last data of the longest track was not correctly added.

Others

- Specific message dialog when loading wrong project type from current project.

- Error when converting a fixed windows track into a variable windows track. (Thank you Kinga)

- Delay after canceling an operation fixed (no more freeze).

- Bug fixed when loading variable windows with chromosomes containing only one value.

- GenPlay checks now if a project is file dependant and if these files are valid (eg: multi genome project and vcf files).

- Behavior change in a variable windows track.
 * If they are not, it will ask for the new path.
 * This verification take place at the loading of a project.

- Rectangles disappear on a low zoom level using variable windows.
 * The score of the window is 0 if the cursor is at the last position + 1 of the window.
 * Previously, the score at this position was the score of the window.
 * It basically showed that the track was going one position further than it actually does.

- Genome position/screen position calculation methods improved.

- Mouse pointer precision (fixes many odd behaviors).

- Windows behavior has changed during the track loading (some action are disabled during the action processing).

Multi Genome

VCF Loader

- Raw name and nickname combo boxes behavior improved:

Multi Genome Dialog Properties
 * Raw names box updated when selecting a file.
 * Nickname box automatically updated (with the raw name value) when the raw names box is updated.
 * Nickname automatically selected at the first change ONLY of a raw name box.

- The multi genome properties dialog is now reachable from the new button on the bottom left of GenPlay.

- New dialogs for selecting stripes and filters. Stripes/Filters are now much easier to create.

- When editing a stripe (after it has been created), it is actually possible to select more than one genome which does not make sense. A message dialog shows up telling the first selected genome only has been taken into account.

- New GT (genotype) filters using heterozygote/homozygote and phasing options.

- For FORMAT fields, can select several genomes and apply operators according to the field type (AND, OR, SUM, MEAN). It manages how data from the different genomes has to behave in order to pass thourgh the filter.

- Statistics for VCF files and their genomes are now processed when loading the files and available in the Multi Genome Dialog Properties at:

- All tables in the Multi Genome Dialog Properties were editable, they are not anymore.
 * -> Files
 * --> "Your file"
 * ---> Statistics

- The default section to open in the dialog can be changed in the settings section.

- The group default text for VCF Loader can be changed in the settings section.

- The dialog can be launch from the regular button. However, a right click on it will popup the different main sections of the dialog as shortcuts!

- The action aiming the update of SNPs, filters and track display has been improved. Threads inter-communication is better and gets the operation faster.

VCF Reading

- Error when reading the header of VCF file that causes an issue in showing the genome raw names within the VCF Loader.

- There was a bug when parsing meta data with comma in Description field, it has been fixed.

GenPlay data structure

- Many changes in packages structure.

- New generic comparator for lists.

- Images access improved.

- New color chooser dialog. Previous colors are now available in the "Recent" panel of the dialog.

- Refactoring of the horizontal scroll bar and the multi genome button, they are now in the same panel.

- A complete refactoring of the communication between the different components of the main frame.

- Unix/Windows temporary files system improved. GenPlay configuration files are now stored in a smarter way.

- New configuration file management (for the application, for the recent project, for the project saving/loading).

- Data structure for VCF files management has changed and is now easier to handle and to improve.

- Use of the enum VCFColumnName (CHROM, POS, REF....FORMAT) in the whole project, generic behavior improved.

GenPlay v533
Release date: 02-10-2012

Download: jar file

VCF Loader changes: - Column order changed (File/Raw/Genome/Group names).

- "Genome" column name is now "Nickname".

- "Group 1" is the default name of a group (even when you add a row).

- Click wherever you want on "Add…" line to add a text/file.

- When adding a vcf file, file chooser dialog automatically set on .vcf.gz file extension).

- Error management behavior: you can edit your settings, having errors and it will be validate when you click "ok" (you will have a message warning you and statistics panel will not update). However, you cannot create the project until your settings are valid.

Multi Genome Improvements:

- Letters centered on the stripes.

- Highlighting precision for SNPs increased.

- Variant navigation improvements.

- Stripes default transparency changed.

GenPlay v529
Release date: 01-27-2012

Download: jar file

Bug fixes:

- Description field of VCF IDs.

- Calculation of the length in the dialog tool tip stripe corrected.

- 1-based DNA sequence bug fixed!

Minor fixes...

GenPlay v527
Release date: 01-25-2012

Download: jar file

Display improvements:

- Draws the border of stripes.

- Write nucleotides over stripes.

These options can be set in the MG properties dialog.

GenPlay v526
Release date: 01-23-2012

Download: jar file

Many bugs fixed:

- Name of human assemblies: GRCh and NCBI ("chr" pattern present/absent).

- 2bit files display.

- 2bit files and 0/1based pair issue.

- DBSNP hyperlink.

- Do not crash when change chromosome.

- GenPlay compatibility with VCF specification 4.0 and 4.1.

- Dialog for general properties of a multi genome project.

- MG project saving/loading.

- Display of the "blank of synchronization" for nucleotide list.

- Variation type automatically enable/disable for stripes editing.

XML import setting improvement for MG project.

The XML setting file can now refer to files with a relative path.

The input file="C:\MyFolder\MyVCF.vcf.gz" can be written: file=".\MyVCF.vcf.gz"

VCF files can be hierarchize into subdirectories.

The only matter is the XML setting file must be at the root directory.

Export feature writes the full path of the files since they can be located in other folders.

A user can store its data like this:

C:\MySettings\       (contains all XML files)

C:\MyVCFs\           (contains all VCF files)

GenPlay v494
Release date: 11-17-2011

Download: jar file

- Implementation of a new navigation dialog for variant stripe.

As before it allows to move backward/forward into the displayed variant list.

It shows all details of the variant that are present into the original VCF file.

- Legend feature for multi-genome stripes.

- Legend activation/deactivation from the option dialog.

- New dialog for the VCF loader.

Chromosome comparator improvements.

Takes into account number in names, no matter the pattern:

e.g.(1):

Group1

Group2

Group10

e.g.(2):

Scaffold1_a

Scaffold2_a

Scaffold10_a

GenPlay v470
Release date: 11-01-2011

Download: jar file

- SNPs position bug fixed.

- Minor fixes.

GenPlay v467
Release date: 10-26-2011

Download: jar file

- Managers have been refactored and many classes are now more optimized.

- Many updates have been made on several classes.

- Minor fixes.

GenPlay v464
Release date: 10-19-2011

Download: jar file

- Schizosaccharomyces pombe assembly added.

- Modification of the pattern of all managers.

The way they communicate each others will change.

- Bug on random extraction corrected.

- Bugs on Multi Genome corrected.

- Extract random lines in file done.

- Fixed window track score sum at loading added to history.

- Major bug 0000017 corrected.

GenPlay v450
Release date: 09-07-2011

Download: jar file

- Bug on chromosome manager iterator corrected (causing problem when displaying last chromosome).

GenPlay v449
Release date: 09-02-2011

Download: jar file

- Bug when copying a multi-curve track solved.

- Bug save multi-curve solver.

GenPlay v447
Release date: 09-01-2011

Download: jar file

- Bug on case sensitivity corrected.

- Bug artifactual peaks when data position greater than last position corrected.

- Bug default chromosome list not set in project frame resolved.

GenPlay v445
Release date: 08-30-2011

Download: jar file

- Bug export executable jar resolved.

- Nicolas added to license javadoc.

- Configuration manager corrected.

GenPlay v442
Release date: 08-29-2011

Download: jar file

- Bug recent project load resolved.

- Bug operation pool resolved.

- Bug genelist resolved.

- Bug genelisttrackgraphics resolved.

- Save Multi Genome project works + bug correction.

- Select sequence file when the file has been moved between a load/save project.

- Bug when no chromosomes selected for a new project corrected.

- Hide the project frame before loading a file.

- Fix bug on SNP management and improve the Chromosome Chooser Dialog.

- SNPs are automatically loaded/released in the RAM.

- New project for single project done.

- Projectframe cleaned.

- Launcher simplified.

- Javadoc corrected.

- Improvement of some VCF file type according to the version 4.0 of VCF.

- Highlighting of the null pointer exception generates by the CHROMOSOME_LOADING_OPTION set to SEQUENTIAL.

- Bug load strip Multi Genome solved.

- Bug memory bar solved.

- Load and save project updated.

- Chromosome selection panel corrected.

- Bug foreign date corrected.

- DAS window redone.

- Deep algorithm and display optimizations in order to increase speed and memory usage.

- Sam library added to the class path

- Bug DAS server corrected.

GenPlay v353
Release date: 05-26-2011

Download: jar file

- Bug repartition around start corrected.