TASUKE+ ver.202009xx (stable) (September xx, 2020)
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* Improved function to display GT:1/2 variant.

* Implemented function to highlight variants for specific Genes.

* Implemented function to filter variants by SnpEff Impact level.

* Supports registration of a large number of Chr/Contig reference seqs. ( >1000)

* Speed up some functions.

* Several Bug fixes.  

TASUKE+ ver.20200305 (stable) (March 5, 2020)
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* Implemented function to highlight the searched genomic region.

* Implemented function to display Blast result on Track.

* Improved so that different external links can be set for each tracks.

* Speed up some functions.

* Several Bug fixes.


TASUKE+ ver.20190826 (stable) (August 26, 2019)
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* Change webStorage from localStorage to sessionStorage

* Speed up some functions

* Several Bug fixes


TASUKE+ ver.20190328 (beta) (March 28, 2019)
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* Improvement:create GWAS manhattan plot when opening GWAS dialog. You can use many functions on GWAS manhattan plot. Please see GWAS function page.

* Improvement:get fasta and create phylogenetic tree faster. You can get fasta and create phylogenetic tree on a few seconds.

* Improvement:Import variant information with snpEFF ANN feature. You can import variant information with snpEFF ANN feature on TASUKE database.

* Several Bug fixes


TASUKE+ ver.20180720 (stable) release. (July 20, 2018)
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* New feature: Create GWAS track with your GWAS data.

* Improvement:Implemented the ePCR option for Primer prediction. Using this option, you can check the specificity of primers predicted by primer3

* Several Bug fixes

TASUKE 1.5.2 release. (October 04, 2016)
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* Change: The method of drawing annotation track table is changed.

* Bug fix: The wrong name is sometimes printed when annotation track is zoomed.


TASUKE 1.5.1 release. (September 09, 2016)
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* Change: The description of Row column options on Track manager is changed from "1" and "4" to "fold" and "expand".

* Bug fix: Function of phylogenetic tree analysis on Tools was fixed.

* Bug fix:"|(pipe)" is usable in GFF file used for visualization of annotation track table.


TASUKE 1.5.0 release. (February 22, 2016)
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* New feature: Multiple condition of general purpose data.
Set multiple condition data to general purpose track of each accession, and this feature shows the data by multiple rows on each accession.
Users can be show a time series or tissue data on TASUKE.

* Change: You can set any colors to each accession group.

* Change: A progress bar was added for wait time of loading the top-page.

* Change: View of accession name and group.
Letters of accession name/group that are beyond the canvas and the letters are automatically trimmed.
And  '~'  will be added to that tail.

* Bug fix: Incorrect group names were generated by phlogenetic analysis.

* Bug fix: Content of VCF and GFF file have " or ', installation process was failed.

* Bug fix: Sometime, any block detail information shows incorrect contents.

* Bug fix: Environment of user-side is automatically loaded when configuration file of server-side was changed.

* Several tiny bug fixes.


TASUKE 1.4.0 release. (October 21, 2015)
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* New feature: Phylogenetic analysis
Making phylogenetic tree from any genomic region.
Set transcript id to the dialog window, you can get a tree from CDS region.
In addition, you can get order of accessions sorted based on the phylogenetic tree.
(PHYLIP software is required for use the feature.)

* New feature: Cacheing system using Redis (beta)

* New function: Cuffdiff to GFF 
tasuke_cuffdifftoGFF.pl:
It converts result of cuffdiff to GFF file.
Set the file to the database, significant region will be highlighted.

* New function: Creating order of accessions by genetic distance
tasuke_sort_by_distance.pl:
This tool make a file for order of accessions. It has 2 method for getting genetic distance.
Copy the file to /TASUKE_HOME/conf/, then the order of accessions is sorted based on the file.

 Number of variants: Sorting by number of variants between reference and each accessions.
 PHYLIP dnadist: Sorting by a phylogenetic tree from result of PHYLIP.

* New function: Upload/download order of accessions by using accession manager

* New function: Automatic installation tool
This tool automatically detects dataset for TASUKE. 
And it loads any dataset to the database.

* New function: Selecting accession from external webpage
Set destination accessions to a localstorage, these accessions only appear.

* Improvement: Support for Oracle database
For more reliability and high performance, you can use Oracle database as backend database.
We recommends oracle database version 11 or later.
If you have enterprise edition, you can use a scripts for database compression.

For more detail: http://tasuke.dna.affrc.go.jp/installation.html#oracle

* Improvement: Support for snpEff 4.x
Run snpEFF with '-classic' and '-formatEff' options.

* Improvement: More robust security 

* Improvement: Compressed web storage
The real local storage capacity is changed 5 MB to 15 MB. And it can accept about 3000 accessions.

* Change: Detail window from annotation track
Click on a GFF object  on annotation track, detail window appears.

* Change: In tasuke_init.pl and tasuke_accession.pl, you can terminate these installation process by 'ctrl+c'.

* Change: Additional messages for install process.

* Bug fix: Contents height was incorrect in a certain case.

* Several tiny bug fixes.



TASUKE 1.3.1 release. (April 18, 2015)
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* Bug fix: Generating a FASTA file feature did not work in some condition.



TASUKE 1.3.0 release. (April 13, 2015)
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* New feature: General purpose track (Custom track)
TASUKE can accept BAM, BED and BEDGraph file as general purpose track for various NGS analysis data.

* New feature: Partitioned data transmission
It loads visible accession only on a web browser. Scroll the browser, it automatically loads from database. However, invisible accessions does not load. This feature reduced loading time, and it can accept a lot more accessions.

* New feature: Color manager for each data
You can set color definition and gradient for each data.

* New function: Browser cache collision avoid system

* New function: Moving to the destination region by URL parameter.

* New function: More detail setting for external link on the annotation track.

* New function: Feature IDs on the annotation track are always view or not
Turning on this mode, it shows the feature IDs below the object. This mode will be turned off when the IDs collision is occured.

* New function: Sorting the accessions on the accession manager.
Click the tabs on accession manager, and the accession list is sorted.

*  New feature: A database schema upgrading tool.
When you want to update the TASUKE, run this tool for upgrading the database. After this processing is finished, you can use the new features.

* Change: Reference sequence name is always viewed.

* Change: Index of an annotation track table.

* Bug fix: Page scrolling on a web browser collisioning with mouse event of the TASUKE.

* Bug fix : Creating TSV file was failed when a BAM file does not include read mapped registered sequence.

* Several tiny bug fixes.



TASUKE 1.2.0 release. (September 1, 2014)
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* New feature: Primer designing
  You can get primer pairs and sequence for designing primer on the Primer3 web interface.
  In case of getting primer pairs, Primer3 is required on your server.
  It requires version 2.3.0 or later.
  And set primer3 path to the configuration file of TASUKE (conf/config.php).
  
  For primer designing, there are two ways of running primer3.
  * menu:tool => PRIMER3 => Set parameter => Run
  * A target variant site on block => pick primer => Set parameter => Run

  If the primer3 does not work on TASUKE, try following commands.
  0. $ yum install policycoreutils-python 
  1. $ semanege tcontext -a -s system_u  -t httpd_sys_content PRIMER3_DIRECTORY
  2. $ restorecon -RF PRIMER3_DIRECTORY

* Function of moving position to target became easier to work.

* Variant detail information became easy to see.

* Bug fix : Creating depth file.

* Bug fix : Loading reference sequence was failed when the name includes white space.

* Bug fix : Nothing was Loaded when VCF file has the unregistered chromosome.

* Bug fix : When the number of accessions is less than 5, menus were hidden by a SNP density object. 

* Bug fix : A block size indicator chases the scroll position on the browser.



TASUKE 1.1.0 release. (May 12, 2014)
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* New feature: Moving to target region by Drag and Drop on the position meter.

* New feature: An animation was added when loading data from database.

* Improvement: Loading time from database was significantly reduced.

* Depth file is not required for viewing detail information.



TASUKE 1.0.0 release. (March 12, 2014)
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* New feature : Showing each variants by real position.
  It came to be able to show each variants variants by real position.
  You can see that by clicking on frequency button of view mode on the top menu.

* New feature : Searching annotations by keyword
  You can search annotations by keyword. Search results appears on dialog box.
  The function uses ID and Note tag in GFF file which is target of search.
  *If you want to use this function, try running tasuke_track.pl(in this version) again.
  
* New feature : Accession management tool is become flexible.
  [tasule_init.pl] : This tool initialize database for TASUKE.
  [tasuke_accession.pl] : This tool has 3 functions. Addition of accession, updating accession information and deleting accession.
  
* New feature : Fine tunable zoom level.
  New controller is available.
  
* New feature : Order of accession
  You can change the order of accession by writing accession_ID on "order.conf".
  
	1) If you do not set accession_ID to order.conf, all accession will be seen on browser. 
	2) Only defined accession by accession.pl is viewed. Others will be ignored.
	3) The accession_ID will be ignored when same accession_ID is found.
	
	For example.
	----DB-----|--order.conf-|--on browser--
	| sample1  |   sample2   |   sample2   |
	| sample2  |   sample2   |   sample4   |
	| sample3  |   sample4   |             |
	| sample4  |   sample5   |             |
	----------------------------------------

* Improvement : TASUKE can accept VCF and multiple sample VCF file generated by GATK(1.6.x or 2.x).

* Improvement : Support for PHP 5.5

* Improvement : Support for Safari on iOS

* Indicator is draggable on browser.

* "snpEff", "Reset" and "Block" buttons were relocated.

* The Color of SNP effect(by snpEFF) is changed white to light green.

* Bug fix : If you installed only few accessions, the block information was truncated.

* Bug fix : tasuke_depth_db.pl was failed depend on server environment.

* Bug fix : View of a chromosome.

* Bug fix : Design of a indicator.

* Bug fix : Moving to next 1/4-window.

* Bug fix : The variant which has error information of snpEFF was not installed in database.

* Bug fix : Clicking on the block which has only depth, then previous snp/indel information appears.

* Bug fix : View of screen message.



TASUKE 0.8.4 release. (October 15, 2013)
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* Bug fix : When you click  SNP/INDEL-block, you can't view a part of detail informations.



TASUKE 0.8.3 release. (October 11, 2013)
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* Bug fix : Maximum of depth value for display was disabled.



TASUKE 0.8.2 release. (September 13, 2013)
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* Improvement : Depth installation tool
  The new install process is 3 to 10 times faster than "tasuke_depth_vcf.pl".
  [tasuke_bamtodepth.pl] : Convert bam file to tasuke-depth formatted file(depth information for the MySQL database).
  [tasuke_depth_db.pl] : Install tasuke-depth formatted file in MySQL database using this tool.
  
  View detail : http://tasuke.dna.affrc.go.jp/index.php/Installation
  
* The controller, variant filter and indicator for depth and variants are integrated into floating box.

* Added an option for the "Export FASTA". The option can be set line width.

* Added a dialog box for "Change reference" feature.

* Bug fix : Indicator on view mode of depth.

* Bug fix : Blank line at beginning of download file.

* Bug fix : Background color and canvas are broken when horizontal scrolling.



TASUKE 0.8.1 release. (July 4, 2013)
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* New feature : Export FASTA
  The fasta file being exported shows preferentially variant type allele regardless of its genotype gheterozygous or homozygoush.
  Ns in the alignment indicates unmapped site (Depth = 0) as well as site below the threshold of depth and quality user set. 

* Added "GO" buttom on a Search & Jump dialog.

* Bug fix : Display of insertion sequence on view of 1bp Scale.

* Bug fix : Reverse complement of reference sequence.

* Bug fix : Track display and message of search by postion or annotation ID.



TASUKE 0.8.0 release. (May 20, 2013)
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This is the first release of TASUKE.
