Difference between revisions of "Release Notes"
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Revision as of 16:59, 14 May 2012
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.
Contents
Current Version
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.
Older Versions
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.
Archived Versions
<listoldgenplaydir/> <webstart/>