Release Notes

From GenPlay, Einstein Genome Analyzer

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Here is a list of the older versions of GenPlay. Older versions of GenPlay can be launched or downloaded on the "Launch or Download Multi-Plateform Jar" section of the Downloads page.

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). The GenPlay version number is indicated on the upper-left corner of the title bar of the main GenPlay application window.


Current Version

GenPlay v1.1.0

Release date: 06-26-2014

- Minimum method to score a gene exons using the scores of a window layer added

- Operation that compares 2 nucleotide layers and display the differences added

- The help page can now be directly accessed from most operations of the contextual menu by clicking on an operation while pressing the Alt key

- Bug where nucleotide list were 1bp off now corrected

- Bug on the score distribution around start operation corrected

- Bug on the score exon function using the maximum operation corrected

- bug where the paternal allele of a variant layer would disappear when the track is resized to its minimal size corrected

Older Versions

GenPlay v1.0.14

Release date: 06-03-2014

- Various multi-genome bug fixes

GenPlay v1.0.12

Release date: 05-07-2014

- GRCh38 and hg38 assemblies added

- a. thaliana assembly added

- When loading a multi-genome XML config files, GenPlay now searches for VCF files inside the XML directory if the VCF files are not found

- Bug when loading SAM/BAM files with custom strand settings corrected

- Bug when copying and pasting between different instances of GenPlay corrected

- Error reports are now correctly sent

- Bug when there is a variant at position 0 in a VCF file corrected

- Bug where fixed window tracks are 1bp shifted corrected

- The progress bar is now correctly displayed during GPTF file loading

- Gene layer in multi-genome project are now correctly displayed (the display of the exons of genes spaning insertions was not correct)

GenPlay v1.0.9

Release date: 04-08-2014

- Various multi-genome bug corrections.

GenPlay v1.0.7

Release date: 03-28-2014

- Legend display bug corrected.

- Variant display bug corrected.

- Variant layer names in the track legend corrected.

- Bug when showing filtered out variations corrected.

- Memory status bar now correctly displayed.

- Track names are now properly saved when a project is saved.

- Sequence layers now correctly display end of chromosomes in Multi-Genome (MG) projects.

- Bug length of indels corrected (was 1bp too long).

- Bug when MG project was saved on a network drive corrected.

- Bug when the mouse was over a variant and the variant was not highlighted corrected.

- Bug when MG projects were saved twice and then cannot be loaded from a different location corrected.

- Bug when converting variant layers into Variable Window layers corrected.

- Bug when exporting a variant layer as VCF file corrected.

- Menu bar now correctly locked during operations.

- Bookmarks now correctly displayed after a project has been loaded.

- Layer names more consistent in the different menus (Variable/Fixed Window layers).

- Some display problems in the new project window corrected.

- Various other bug corrections and display improvements.

GenPlay v1.0.5

Release date: 03-12-2014

- File chooser dialog bug corrected.

- Bug when opening the contextual menu of sequence track corrected.


GenPlay v1.0.4

Release date: 02-28-2014

- Multigenome GUI improved

- Other part of the user interface has been improved, specially for Nimbus and Mac look and feels

- Mac integration enhanced

- Various multigenome bugs fixed


GenPlay v1.0.3

Release date: 02-10-2014

- Option to save an entire track added

- GPTF extension for GenPlay track files added

- GenPlay Quick View can be used to visualize GPTF files

- A main menu bar can be showed / hidden from the option menu

- Regions of the genome can now be bookmarked

- Save as option added for project

- GUI improved (new buttons, new icons, new default theme)

- The content of a track can now be cut and paste as text, image or file in text editors, image editors or file browsers

- Bug when visualizing the sequence of an insertion in multi-genome corrected


GenPlay v1.0.2

Release date: 01-28-2014

- Project extension changed to GPPF to avoid conflicts with other applications

- File sorter added, unsorted files can now be loaded

- Cut and paste between different instances of GenPlay or between GenPlay and Windows are now possible

- OSX Integration (main menu bar added, icons correctly displayed, new option to select the memory allocated, default folder bug corrected)

- The memory allocated to GenPlay can now be modified from within the application (OSX only)

- Bug where the configuration would disappear corrected

- Fixed step wiggle files are now correctly loaded


GenPlay v1.0.1

Release date: 01-22-2014

- Update menu item added to main menu bar (Windows only)

- GenPlay project file extension switched to .gpf


GenPlay v996

Release date: 01-09-2014

- 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

- Bugs on gene layer / extract exons operation corrected

- Bugs on gene layer / extract intervals operation corrected


GenPlay v976

Release date: 09-24-2013

- Multi-genome bugs corrected

- OSX integration improved


GenPlay v972

Release date: 09-10-2013

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

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

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).

  • If they are not, it will ask for the new path.
  • This verification take place at the loading of a project.

- Behavior change in a variable windows track.

  • 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.

- Rectangles disappear on a low zoom level using variable windows.

- 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:

  • 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.

Multi Genome Dialog Properties

- 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:

  • -> Files
  • --> "Your file"
  • ---> Statistics

- All tables in the Multi Genome Dialog Properties were editable, they are not anymore.

- 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

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

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

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

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

- 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

- SNPs position bug fixed.

- Minor fixes.


GenPlay v467

Release date: 10-26-2011

- 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

- 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

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


GenPlay v449

Release date: 09-02-2011

- Bug when copying a multi-curve track solved.

- Bug save multi-curve solver.


GenPlay v447

Release date: 09-01-2011

- 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

- Bug export executable jar resolved.

- Nicolas added to license javadoc.

- Configuration manager corrected.


GenPlay v442

Release date: 08-29-2011

- 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

- Bug repartition around start corrected.