TASSEL Changelog

What's new in TASSEL 5.2.92

Nov 10, 2023

New phg.jar v1.8
Update postgresql-9.4-1201.jdbc41.jar to postgresql-42.6.0.jar

New in TASSEL 5.2.91 (Oct 24, 2023)

New in TASSEL 5.2.90 (Jul 11, 2023)

New in TASSEL 5.2.89 (May 20, 2023)

New in TASSEL 5.2.88 (Mar 14, 2023)

New in TASSEL 5.2.87 (Jan 10, 2023)

New in TASSEL 5.2.86 (Oct 11, 2022)

New in TASSEL 5.2.85 (Sep 22, 2022)

New in TASSEL 5.2.84 (Aug 31, 2022)

New in TASSEL 5.2.83 (Aug 4, 2022)

New in TASSEL 5.2.82 (Jun 17, 2022)

New in TASSEL 5.2.81 (Apr 8, 2022)

New in TASSEL 5.2.80 (Feb 17, 2022)

New in TASSEL 5.2.79 (Jan 19, 2022)

New in TASSEL 5.2.78 (Nov 16, 2021)

New in TASSEL 5.2.77 (Oct 27, 2021)

New in TASSEL 5.2.76 (Oct 27, 2021)

New in TASSEL 5.2.75 (Oct 4, 2021)

New in TASSEL 5.2.74 (Sep 11, 2021)

New in TASSEL 5.2.73 (Jun 23, 2021)

New in TASSEL 5.2.72 (Apr 8, 2021)

New in TASSEL 5.2.71 (Mar 26, 2021)

New in TASSEL 5.2.70 (Feb 11, 2021)

New in TASSEL 5.2.69 (Jan 15, 2021)

New in TASSEL 5.2.68 (Jan 8, 2021)

New in TASSEL 5.2.67 (Nov 10, 2020)

New in TASSEL 5.2.66 (Oct 29, 2020)

New in TASSEL 5.2.65 (Sep 10, 2020)

New in TASSEL 5.2.64 (Jul 9, 2020)

New in TASSEL 5.2.63 (Jun 15, 2020)

New in TASSEL 5.2.62 (Jun 2, 2020)

New in TASSEL 5.2.61 (May 8, 2020)

New in TASSEL 5.2.60 (Feb 20, 2020)

New in TASSEL 5.2.59 (Dec 12, 2019)

New in TASSEL 5.2.58 (Nov 13, 2019)

New in TASSEL 5.2.57 (Oct 11, 2019)

New in TASSEL 5.2.56 (Sep 18, 2019)

New in TASSEL 5.2.55 (Sep 11, 2019)

New in TASSEL 5.2.54 (Jul 26, 2019)

New in TASSEL 5.2.53 (Jun 28, 2019)

New in TASSEL 5.2.52 (Mar 22, 2019)

New in TASSEL 5.2.51 (Dec 20, 2018)

New in TASSEL 5.2.50 (Oct 26, 2018)

New in TASSEL 5.2.49 (Oct 5, 2018)

New in TASSEL 5.2.48 (Aug 3, 2018)

New in TASSEL 5.2.47 (Jul 27, 2018)

New in TASSEL 5.2.46 (Jul 20, 2018)

New in TASSEL 5.2.45 (Jul 13, 2018)

New in TASSEL 5.2.44 (May 18, 2018)

New in TASSEL 5.2.43 (Apr 3, 2018)

New in TASSEL 5.2.3 (Feb 7, 2015)

New in TASSEL 5.2.2 (Feb 7, 2015)

Fixed bug with GenotypeTableBuilder.getInstanceOnlyMajorMinor(), that caused "Remove minor SNP states" from working correctly in Sites Filter.
Added -e ignore option for unspecified restriction enzyme. In this case barcodes and common adapter start sequences will be recognized, but chimeric DNA fragments (or partial digests) will not be trimmed.
TAS-381 Cleaned up FisherExact.java, removed commented out lines, altered resizeArrays to make more efficient.
TAS-378 Continued implementation of CombineGenotypeTable
write function in TagsOnGeneticMap
TAS-503 SNPQualityProfilerPlugin now actually does some profiling of the SNP quality.
TAS-381 FischerExact:resizeArray() Added missing code to redeclare array with new size before calculating array values.
TAS-381 Make FisherExact a singleton, add resizing factorial arrays.
TAS-399 Changed GeneratePluginCode to use variable name for method signatures instead of GUI Name.
TAS-611 Corrects values used for degrees of freedom in calculation of p-values for additive and dominance terms in DiscreteSitesTest and comments out 3 lines of debug code in AbstractFixedEffectLM
Added MslI. Fixed MspI common Y-adapters to match Poland et al. 2012. Added PstI-MspI-GDFcustom.
TAS-511 Added attributeStream() to Phenotype and subclasses and added method to remove observations with any missing values to PhenotypeBuilder. The changes were made to make it easier to test EqtlAssociationPlugin but should be useful for other applications as well.
TAS-511 deleted function using ReferenceProbabilitySpliterator
TAS-511 further implements EqtlAssociationPlugin and removes ReferenceProbabilitySpliterator
sort function in TagsOnGeneticMap
TAS-578 Initial implementation of export / import TaxaList
fixes bugs with save to file option in CompressedMLMusingDoubleMatrix
TAS-511 Additional work on EqtlAssociationPlugin implementation.
TAS-503 Concepts for SNPQualityProfilerPlugin.
TAS-591 Clarification of methods. Corrected bug with invariant cutPositions.
TAS-571 Correcting command line parameters with same prefix. Changed proportion to go from 0 to 1.
TAS-591 Requesting comment/clarification for findAlleleByAlignment. If the syntax of "//TODO TAS-591" is not correct, please let me know.
TAS-511 start of matrix eqtl plugin implementation
TAS-511 Fixed errors in SolveByOrthogonalizing so that it passes unit tests. Apply to permutation testing in AbstractFixedEffectLM.
TAS-488 Continue improving Hapmap Importing Error Messages.
TAS-563 PluginParameter for choosing from a runtime list.
TAS-371 Added helpful message to ProductionPipeline for if user points to a directory without subdirectories
TAS-511 Fix bug and add ability to solve add plus dom models to SolveByOrthogonalizing
In DiscreteSitesFELM, if F = Infinity (usually because df = 0) set F = NaN and p = NaN.
fixes bug in PhenotypeBuilder that was failing to set "NaN" as missing data in version 4 style trait import
Added Updated ProjectPcsAndRunModelSelectionPlugin from Alex
TAS-573 Improve numerical imputation efficiency
add test for parentPlugin != null in progress bar update in AbstractFixedEffectPlugin
implements progress bar in FixedEffectLinearModelPlugin
TAS-563 Initial implementation: PluginParameter for choosing from a runtime list.
TAS-586 Fixes bugs in permutation code in AbstractFixedEffectLM
TAS-511 SolveByOrthogonalizing is the initial implementation of methods for linear model solving outlined in the matrix Eqtl paper.
TAS-573 adds imputeFromNonMissingNeighbors method which only uses neigbors with non-missing data for the value being imputed.
TAS-571 Added new optional filter variables to SAMToGBSdbPlugin allowing user to specify minimum alignment length and minimum alignment proportion. Methods to calculate are called from parseRow().
TAS-582 Added taxa name to phenotype import error message in PhenotypeBuilder.ImportPhenotypeFile()
TAS-577 Implements spliterator that iterates through ReferenceProbability by site as ReferenceProbabilitySpliterator. Adds a method to GenotypeTableUtils that uses that to create a stream.
TAS-582 Make Numerical Import functions consistently accept only NA, NaN, and . as Unknown values.
TAS-456 Changed Data Menu option name from "Transform" to "Transform Phenotype". And improved error message when incorrect input selected.
TAS-456 removed obsolete class src/net/maizegenetics/analysis/numericaltransform/Conversion.java
TAS-456 Removed obsolete class KNN

New in TASSEL 5.2.1 (Feb 7, 2015)

New in TASSEL 5.2.0 (Feb 7, 2015)

TAS-533 adds code to FilterTraitsPlugin and TasselPipeline to handle -excludeLastTrait pipeline flag.
TAS-428 Validated PCA. Made a change to PrinComp to get output to exactly match R method prcomp. Finished implementing
TAS-565 Override contains for PositionArrayList
TAS-544 Support different Illumina quality score strategies
TAS-544 Eliminate tags not found multiple times in flowcell
TAS-564 Fixed problems with ModifyTBTHDF5Plugin and SeqToTBTHDF5Plugin where checking for optional parameters failed because the value was empty string instead of null.
TAS-559 Changed new getSNPPositionsForChromsomes() method to return PositionList. Added parameter validation.
TAS-559 Added new class PositionListIOUtils with initial method to read the SNP Conserve File.
TAS-428 fixed bug in PhenotypeBuilder that caused intersect join to give incorrect results depending on the order in which the phenotypes were joined.
Fixed a typo in the usage statement
TAS-456 Moved numerical imputation from the Data menu to the Impute menu.
TAS-555 fix MLM handling of ReferenceProbability
TAS-559 Code to pull SNPs for a specified chromosome from the database. This should be under a separate issue, but I thought I was creating an issue and instead got a sub-task.
TAS-428 correct bug in CompressedMLMusingDoubleMatrix to print correct residuals
TAS-334 implemented alleleDefinitions() and alleleDefinitions() in TOPMGenotypeTable.
TAS-40 Added more user friendly error messages to ReferenceProbabilityBuilder and SiteScoreUtils.
TAS-428 Added code to importing phenotypes to recognize "NA" and more user friendly error message.
TAS-456 Changed tool tip for TransformDataPlugin.
TAS-456 Deprecate KNN class.
TAS-428 added getters and setters to PrincipalComponentsPlugin
TAS-428 finished implementation of PCA in the PrincipalComponentsPlugin. Corrected handling of missing neighbor data in kNearestNeighbors.
TAS-554 Corrected implementation of depth(), dosage(), alleleProbability() and referenceProbability() in FilterGenotypeTable.
TAS-428 Fixed a type conversion error and add meaningful name and comments to output
TAS-428 Implement plugins for data transformation: NumericalGenotypePlugin and TransformDataPlugin. Adds them to the Data menu.
TAS-456 Added Numerical Transform classes from Janu
TAS-552 Make Float.NaN is ReferenceProbability view has gray color
TAS-428 made conversion methods public in NumericalGenotypePlugin
TAS-552 Change color range for heat maps to be easier to read text when values are 0.
TAS-428 added stream methods to Phenotype to create Streams of attributes of a given ATTRIBUTE_TYPE. Implemented the new methods in CorePhenotype and FilterPhenotype. Added a method to convert a FilterPhenotype to a CorePhenotype.
TAS-428 Modified TaxaAttribute so that the name is always "Taxa".
TAS-428 Finished Phenotype export
TAS-428 Added Transform to data menu, completed TransformDataPlugin and TransformDataDialog, and added code to PhenotypeBuilder to recognize -999 as missing data in phenotype files.
TAS-428 added code for setting output filename for compatibility with TASSEL 4 pipeline
TAS-428 did initial testing of MLM code. This fixes bugs in MLMPlugin and CompressedMLMusingDoubleMatrix so that limited tests using the tutorial data run correctly.
TAS-428 fix a couple of bugs in CompressedMLMusingDoubleMatrix
TAS-428 removed permformFunction method from KinshipPlugin so that it stopped overriding the AbstractPlugin method.
TAS-523 Added -log [] to Tassel Pipeline. Same as -debug except no debug messages.
TAS-428 Commenting out use of ProjectPcsAndRunModelSelectionPlugin until migrated to new Phenotype package.
TAS-428 Removing obsolete net.maizegenetics.trait package
TAS-428 made changes to NumericalTransformPlugin to maintain compatibility with pipeline options.
TAS-521 Fix DiscoveryTBTPlugin:processFastQ to handle Tag build error consistently as per change in commit 321fd6f
TAS-428 debug setAlternateMinorAllelesToMinor in NumericGenotypePlugin
TAS-428 Initial implementation of NumericalGenotypePlugin that creates a ReferenceProbability from nucleotides. Alternative coding schemes including creation of AlleleProbability will be added later. This version should be sufficient for an initial release.
TAS-428 finished implementing TransformDataPlugin and TransformDataDialog. Still need to write junit tests.
TAS-428 move TransformDataDialog and TransformDataPlugin from net.maizegenetics.analysis.data package to net.maizegenetics.analysis.data.numericaltransform
TAS-521 Change SAMToGBSdbPlugin:processData() and parseRow() to ignore Tags that null. BaseEncoder:getLongFromSequence translates a sequence of 32 T's to value -1. This sequence was seen in Zea_may.AGPv3 chromosome files. For now, ignore them.
TAS-521 Change TagBuilder instance(..) code to create a 0 length seq2Bit array instead of returning null when getLongArrayFromSeq() returns null.
THis allows calls to TabBuilder.instance(..).build() to succeed without a null pointer exception. (though the result from build() may be null)
TAS-521 Fix another null pointer exception and clean up unused code.
TAS-521 Continued fixed serious bugs in the TaxaDistribution not incrementing and failed units tests
This works for the smaller taxa distributions
TAS-521: Fix null pointer exception in TaxaDistBuilder.
TAS-428 Initial implementation of Phenotype export
TAS-521 Fixed serious bugs in the TaxaDistribution not incrementing and failed units tests
TAS-521 Approaches testing map size less frequently
TAS-521 Recommit of fixes bug in compression approach of TaxaDistributions
TAS-541 : populated "Effect" from SnpEff output
TAS-521: Changes to TaxaDistExpandable to improve fastQ processing
performance. Trove Library added.
TAS-456 Removed obsolete numerical transform Conversion methods
TAS-456 Removed obsolete numerical transform classes
TAS-456 Corrected class name when getting icon resource in TransformDataPlugin
TAS-177 Altered FILLIN help notification to mention including all sites
TAS-521 Fixes bug in compression approach of TaxaDistributions
If the first taxa was not within the first 256 taxa, it caused a bug.
TAS-521 Method to handle various fast quality score systems
TAS-428 Work on conversion to phenotype package. Fixes error related to use of non-existent NumericAttribute.stream() method.
TAS-428 Add toString() method to PhenotypeAttribute classes that returns name()
TAS-428 work on implementing data transformation
Output change in PanA
Added some new restriction enzymes
TAS-539 Added harmless comment to test commit
TAS-539 Altered LD plugin so command-line default is to treat hets as missing
TAS-531 : minor changes to schema
TAS-518 Functional but not tested version of ProductionSNPCaller for V2
TAS-521 Fix bug in DiscoveryTBTPlugin (v2) processFastQ() that halted reading of the file on a null pointer exception.
TAS-521 one more optimization of DiscoveryTBTPlugin.
TAS-521 Fixed method header comment from last submission.
TAS-521: Reworked BaseEncoder:getSequenceFromLong() to use "append" vs "insert". This improves execution of DiscoveryTBTPlugin by about 9%. Tested for accuracy of converted string via junit testing of the new method, and tested performance via the DiscoveryTBTPluginV2 junit and JProfiler.
TAS-531 : Modified gene table slightly
TAS-428 Added logging message to Tassel Pipeline to warn users that -glm flags are deprecated if those flags are used.
TAS-182 Initial implementation for viewing Projection Genotype Table in GUI.
TAS-518 Initial ProductionSNPCaller for GBSv2
TAS-507 GenomeSequenceBuilder: Added range check to chromosomeSequenceIntInt(), added extraneous text from fasta file Chromosome line to the Chromosome object's annotation list.
TAS-534 : jar for postgresQL jdbc
TAS-531 : added FOREIGN KEY chromosome_id to qtl_peak table
TAS-507 Simplification of compression and chromosome naming
TAS-428 partial implementation of PhenotypeTransformPlugin and TransformDataPlugin
TAS-507 Changes to return empty set if no chromosomes.
TAS-507 chromosome sequence with recording of length
Recording of length is key to simplify the code.
TGAS-507 Removed unused method from GenomeSequenceBuilder
TAS-428 adding NumericalGenotypePlugin in place of GenotypeTransformPlugin
TAS-428 fix bug in PhenotypeBuilder join code that caused joins to fail for some data sets
TAS-428 added code to PhenotypeBuilder to handle -excludeLastTrait pipeline command
TAS-507 Additional changes to GenomeSequenceBuilder, renaming ReferenceGenomeSequence class to HalfByteGenomeSequence and moving functionality out of that class, into the builder.
TAS-532 Updated maxDonorHypotheses help message to indicate that heterozygous taxa need this value to be set very high
TAS-532 Added pluginparameter -impAllHets for FILLIN to impute as hets even when original call is homozygous. Also renamed donorFile to donorDir (since it's now a directory)
TAS-428 TransformDataPlugin created to deal with transformations. It will call either the GenotypeTransformPlugin or the PhenotypeTransferPlugin. Most of the implementation has yet to be done.
TAS-507 Fix for handling unknown allele (N).
remove src/net/maizegenetics/dna/map/ReferenceGenomeSequence.java
TAS-507 Adding GenomeSequenceBuilder, moving ReferenceGenomeSequence class inside the builder.
TAS-428 Debug issues with StepwiseOLSModelFitter conversion
TAS-468 Corrected ProjectionLoadPlugin to not fire data set return event, as abstract class does that.
TAS-398 Added TasselLogging.basicLoggingInfo() that prints basic logging message about system. Used by GUI, CLI, and Logging Dialog.
TAS-428 modified methods to convert genotypes to reference probability to code major allele as 1 to conform to Tassel 4 coding.
TAS-428 Deleted two PCA classes no longer being used. Start implementation of PCA plugin.
TAS-507 More changes to GenomeSequence code. - Added builder class - Javadoc style comments for GenomeSequence interface - Altered ReferenceGenomeSequence read method to return allele/byte.
TAS-531 : initial PostgreSQL schema for storing genome annotations
TAS-428 add methods for converting Genotypes to numerical values
TAS-507 More changes to ReferenceGenomeSequence to add clarity - Changed chromPositionMap to have key type "Chromosome" instead of String. - Expanded GenomeSequence interface comments and changed to javadoc style - Removed "getAlleleEncoding" method, replaced with method from NucleotideAlignmentConstants
TAS-428 added code to handle Tassel 4 style pipeline commands
StepwiseOLSModelFitter, fixed bug that was crashing analysis
TAS-428 Modified GenotypePhenotype TableReport to display short genotype Strings when the genotypes are SiteScores.
TAS-428 Modified exclude all in FilterTraitsDialog so that Taxa are not excluded.
TAS-428 Added method to set random seed for testing permutation
TAS-428 Added getters and setters to FixedEffectLMPlugin
TAS-507 Adding changes I forgot to make on initial submission. For ReferenceGenomeSequence:chromosomeSequence(): - return should be nothing more than the chromEntry value.
TAS-428 Fixes bugs in PhenotypeLM and in PhenotypeBuilder uncovered by unit test. PhenotypeBuilder fixes affect fromFile and fromLists methods.
Initial code for GenomeSequence (interface) and ReferenceGenomeSequence(class). Some of this will change when the GenomeSequenceBuilder is implemented. - GenomeSequence.java: new file defining the interface - ReferenceGenomeSequence.java: new file implementing the functionality - DiscoverySNPCallerPluginV2.java: added keyFile functionality, but have NOT added the new plugin value. Currently only used in junits. - NucleotideAlignmentConstants: added method to grab allele char from number. Used in junits when decoding a byte string.
Still to do: Implement the GenomeSequenceBuilder class.
TAS-428 Implement new version self-describing version of FixedEffectLMPlugin that uses Phenotype package
TAS-428 Correct bugs in handling of Float.Nan in byteToFloatPercentage and floatToBytePercentage
TAS-428 modify FilterGenotypeTable to handle case where the GenotypeCallTable is null
TAS-428 add guess function line in FileLoadPlugin to recognize header as trait file
TAS-428 fix problems uncovered by unit test validation
TAS-527 Corrected Linkage Disequilibrium null pointer exception when accumulate R2 is checked
TAS-428 Converted StepwiseOLSModelFitter and StepwiseOLSModelFitterPlugin to use Phenotype package
Fixed bug in BiparentalHaplotypeFinder and NucleotideImputationUtils that was causing FSFHap to fail if the first marker in a dataset was all missing data.
TAS-502 Completed submitting of the discovery pipeline results to the DB
TAS-428 Convert KinshipPlugin and Kinship class to use Phenotype package. Change KinshipPlugin to self-describing and delete KinshipMethodDialog.
TAS-428 Convert RidgeRegression to use Phenotype package classes instead of trait package classes. Add static method to AssociationUtils to convert a primitive double array to a float array.
TAS-514 Add support for GenotypePhenotype when adding GenotypeTable as parameter. Also add support to limit which components of a GenotypeTable are allowed for that parameter.
TAS-514 Add support to PluginParameter to select a component (i.e. Genotype, ReferenceProbability, Dosage, Depth, AlleleProbability) from a given GenotypeTable.
TAS-428 Changed FilterTraitsDialog and FilterTraitsPlugin to use Phenotype package
TAS-428 Fix bug in GenotypePhenotype. getTableColumnNames() was returning null.
TAS-453 : added the option keepTempGenotypes.
So you don't have to re-extract the taxa if you are working with a full set of flowcell lanes for a project (e.g., running maize landrace families from 13FL from Rare Alleles C2.1).
TAS-428 Made changes to implement fixed effect linear models using the Phenotype package.
TAS-428 Converted MLM to use Phenotype package and site scores. Moved public static methods from AbstractFixedEffectLM to AssociationUtils.
TAS-501 Initial support for recording the direction of alignment in GBSdb
TAS-428 move TableReport creation from instantiating classes to AbstractFixedEffectLM. Fix some bugs uncovered by junit tests.
TAS-428 Convert UnionAlignmentPlugin to use Phenotype package.
TAS-524 Updated FSFHap documentation to show how to run it from the command line.
TAS-428 Convert DataTreePanel to use Phenotype package.
TAS-428 Converted FilterTaxaAlignmentPlugin to Phenotype package.
TAS -428 Converted net.maizegenetics.analysis.data package from net.maizegenetics.trait to net.maizegenetics.phenotype
TAS-501 Adding functionality for tags that do not map, and reverse complement tags
TAS-523 Add option to send Tassel pipeline to a file (-debug )
TAS-428 implement PhenotypeLM a class that takes a Phenotype as input then tests whether taxa are significantly different and generates BLUEs for the taxa
TAS-103 : No longer moves fastq files when they were not actually analyzed (for example, if the ready.txt file was not present)
TAS-428 continued implementation of GLM classes that use the Phenotype package
add toArray methods to DoubleMatrix
TAS-391 Changing of AtomicLong use to LongAdder
TAS-391 General clarifications of GBSv2 pipeline
Fixed bug with DiscoveryPipeline minimum threshold
TAS-511 fixed bugs in DiscreteSitesMatrixFELM, a test implementation of the method from Matrix eQTL.
TAS-428 changes to FixedEffectLM classes to fix problems and some additions to Phenotype package classes related to help implement FixedEffectLM. FixedEffectLM and its derived classes will replace most of the code in FixedEffectLMPlugin once fully implemented and tested.
Added code to skip markers that have no non-missing values. Also deletes a class, DiscreteSitesAddDomWithReplicationFELM, that was never actually used.
TAS-502 Adding database close operations to GBS db
TAS-432 Initial display of ReferenceProbability in Tassel GUI.
TAS-334 More implementation of TOPMGenotypeTable
TAS-500 In ReadNumericMarkerUtils, set physical position same a site number instead of 0.
TAS-491 Redesigned GenotypeTable to make GenotypeCallTable optional. New method hasGenotype() indicates whether the GenotypeTable has genotype values.
TAS-513 Corrected Bug with Genetic Heat Map Colors
TAS-511 Creates class to implement Matrix eQTL method for OLS solution to linear models
Adding new classes and modifying LinearModelUtils and ModelEffectUtils to support new phenotype package and to improve organization of the fixed effect LM models.
Added code to run_pipeline.pl and start_tassel.pl to fix em-dashes when setting minimum and maximum heap size.
TAS-336 Improved formatting of Plugin error messages sent to the GUI.
Improved error message of FastqToTagCountPlugin when no fast files found in input directory.
TAS-502 Completed basic implementation of new SNP caller using DB and lambdas
FIx parameter list to GenotyeCallTable.getInstanceUnknownValues used by ReadNumericeMarkerUtils.
TAS-508 Changed Default "Min not Missing" to 0.0 for FilterTaxaPropertiesPlugin.
TAS-508 Convert FilterTaxaPropertiesPlugin to PlugParameter Design
Corrected Sequence Viewer to not allow reordering of columns.
Add Files.lines() that will work with gz files, and reduce repetitive code by setting the buffer the standard size
TAS-502 Initial redesign of DiscoverySNPCallerPluginV2
TAS-391 Added reference tag support to Tags
TAS-391 Fully support for variable length tags
TAS-504 Trie based barcode processing, encapsulation of enzyme information
TAS-500 Add handling of numerice marker files as genotypes.
TAS-502 Copy DiscoverySNPCaller to new package
TAS-404 Migrate one step TBT class to new package and integrate with TagDataWriter
TAS-501 Implementation of plugins to work with Aligners - export to Fastq, import SAM to DB
TAS-391 Improved Tag classes and builders that deal with variable length tags
TAS-480 Commit of SQLite database adapter
TAS-480 Initial migration of TagData and SQLite implementation
Added ProjectPcsAndRunModelSelectionPlugin to code base for Alex to test. Must comment out one line in FileLoadPlugin to see on GUI.
TAS-40 Moved ALLELE_DEPTH_TYPES from AlleleDepthBuilder to AlleleDepth and made it public. This is for easier iteration over an AlleleProbability instance.
TAS-40 Moved ALLELE_PROBABILITY_TYPES from AlleleProbabiltyBuilder to AlleleProbability and made it public. This is for easier iteration over an AlleleProbability instance.
fixed GLM bug in additive only model
TAS-40 Added ReferenceProbability to GenotypeTable and GenotypeTableBuilder
TAS-40 Changed SiteScoreUtil to handle Float.NaN. byte value 255 is translated to Float.NaN

New in TASSEL 5.1.0 (Feb 7, 2015)

TAS-493 implement separate phenotype on factors and joining when there are multiple observations for some taxa at the same factor levels. The primary purpose of the changes is to support table pivoting.
Added debugging level logging to export hapmap files.
TAS-290 Correct XML creation when flag is self describing plugin
TAS-290 Update TasselPipelineXMLUtil.TAG_STRINGS
TAS-498 Added option to printing usage statements in ListPlugins plugin
TAS-498 Add getUsage() to Plugin Interface
TAS-423 Corrected LinkageDisequilibrium calculation of total number of tests when value greater than max int.
TAS-486 Corrections to GeneralAnnotationStorage reading / writing annotations to HDF5 when there are no annotations.
Fastq read QC and Contiging
TAS-486 : changed the stored annotation names to dataSetName and dataSetDescription. Used the new fxn GeneralAnnotationStorage.writeToHDF5() to write the annotations.
TAS-486 Modified GeneralAnnotationStorage.readFromHDF5 to be more generic, so that it can be used for other data structures (i.e. Position Lists). Also added writeToHDF5 methods for generic writing annotations to HDF5.
TAS-486 : DataSetName & DataSetDescription are now written to and read from an HDF5GenotypeTable
TAS-492 Improved performance of TableReportBuilder when writing to a file.
TAS-453 : added new PluginParameter positionSourceHDF5GenoFile
Reverted last change because I forgot the dash in TAS 453
TAS 453 : added new PluginParameter positionSourceHDF5GenoFile
TAS-497 Fixed bug with LD
TAS-391 Unifying Tag classes with an AbstractTag
Fixes a TaxaDistribution compression bug involving Unsigned byte maximum.
TAS-473 Changes to Phenotype package classes to support table pivoting and subsetting phenotypes by factor levels
Fixes a bug when there is no known variants at a position.
Start code for sequence reads QC and contiging
TAS-492 Initial implementation of TableReportBuilder
TAS-473 Changes to Phenotype package classes to make PhenotypeBuilder more intuitive to use and to partially implement phenotype table pivoting.
TAS-423 In TableReport... public int getRowCount(); change to public long getRowCount(); public int getElementCount(); changed to public long getElementCount(); public Object[] getRow(int row); changed to public Object[] getRow(long row); public Object getValueAt(int row, int col); changed to public Object getValueAt(long row, int col);
TAS-423 Removed methods getTableData() from TableReport Interface and implementations.
TAS-423 Removed use of TableReport.getTableData() from HistogramPanel
TAS-423 Removed use of TableReport.getTableData() from TableReportStatCategoryDataset
TAS-423 Removed use of TableReport.getTableData() from TableReportPieDataset
Removed use of TableReport.getTableData() from Grid2dDisplayPlugin
TAS-423 Removed use of TableReport.getTableData() from TableReportXYDataset
TAS-423 Removed use of TableReport.getTableData() from SynonymizerPlugin.
TAS-423 Removed use of TableReport.getTableData() from DiversityAnalyses.
TAS-423 Removed use of TableReport.getTableData() in TableReportBoxWhiskerCatDataset
TAS-473 Changes to support pivoting phenotype table
TAS-491 Add Empty GenotypeCallTable when no Genotypes (only scores)
TAS-423 Removed unnecessary implementation of TableReport from PolymorphismDistribution.
TAS-486 Starting code for General Annotations of Genotype Tables in HDF5.
TAS-485 : Now sets the dataSetName and dataSetDescription via the new GenotypeTableBuilder methods
TAS-428 changes to Phenotype package classes for use with GLM and MLM
TAS-488 Performance and error messages improvements of Import for Hapmap
TAS-486 Initial implementation of GeneralAnnotations for GenotypeTable.
Removed code in TASSELMainApp that tries to set look and feel to windows. Just letting it be default. Throws an exception every time I can tell anyway.
TAS-415 Refactoring improvements to PLINK import.
TAS-336 Changed convert() method to handle Enum different, so that it compiles in Eclipse. Apparently shouldn't have compiled under Java in the first place. Also, checking if String to String conversion, just return input.
TAS-344 Updated biojava libraries to 4.0.0 (snapshot) and modified forester_1034.jar (Peter fixed so prevent exiting Tassel when closed). I will replace biojava when official 4.0.0 jars are released.
TAS-485 : Now replaces __DATE__ with a yyyyMMdd date stamp in the dataSetDescription as well
TAS-485 : in the output file name, __DATE__ is now replaced with _yyyyMMdd
TAS-419 Changing title of Tassel javaDoc home page from "TASSEL 5.0: JavaDoc" to "TASSEL JavaDoc 5.0", so that searching for "Tassel Javadoc" ranks higher in the search engines.
TAS-487 : bug fix so that HDF5Utils.isHDF5GenotypeLocked() works right
TAS-485 : Almost ready to go, once DataSetName and DataSetDescription annotations can be added via the GenotypeTableBuilder
TAS-103 Changed AbstractPlugin to fireDataSetReturned() even if performFunction() return null. This will allow chaining Plugins when no input needed to start next step.
TAS-485 : Commented out the broken line
TAS-485 : Start of this simple plugin
TAS-485 : added a getBuilder(String existingHDF5File) function for an unfinished HDF5 file
TAS-480 Implementation of TaxaDistribution class that provides roughly 4-fold compression relative to HDF5 TBT
Removed obsolete unused class net.maizegenetics.util.RightJustifiedFormat
Removing obsolete unused classes in net.maizegenetics.util Histogram and IntLinearCongrRandom
TAS-481 Changed Self-Describing Plugins parameter dialog to cancel when clicking X instead of running.
TAS-483 Fixed TaxaListUtils.getAllTaxa() to return a sorted list
TAS-481 Self-Describing Plugin: Limited number of parameters are displayed
TAS-176 fixes a bug that occurred when converting parent calls to nucleotides when the order of taxa in the imputed GenotypeTable is different from that in the original GenotypeTable.
TAS-103 Corrected use of lock file when running Production Pipeline
TAS-103 Added Summary Log File to Production Pipeline. Also changed key file to end with "_key.txt". Also added -ko option to ProductionSNPCallerPlugin executions.
TAS-176 debugging and improving FSFHap, specifically fixes a problem with the subpopulation check
TAS-481 Fixed Self-Describing Plugin: Limited number of parameters are displayed
TAS-371 : ProductionSNPCallerPlugin now adds the taxa annotation "Status" with a default value of "private"
TAS-476 Cleaning up HDF5 experiments in preparation for GBSData interface
TAS-453 : Fixed minor typo
TAS-453 : Added preferredHaplotypeSize to the runFILLIN() method
TAS-479 Remove unneeded AbstractDisplayPlugin.FileFormat
TAS-467 Changed cache size of HDF5ByteGenotypeCallTable back to 1.5 * number of taxa. Needs to be bigger for getting full sites.
TAS-453 : Added updateTaxonAnnotations(Taxon origTaxon, Taxon newTaxon)
TAS-176 FSFHap added to impute menu in GUI. WritePopulationAlignmentPlugin now returns GenotypeTables instead of writing output to a file.
TAS-474 Finished implementing FSFHapImputationPlugin
TAS-336 Added AbstractPlugin.preProcessParameters() method that can be overridden to process parameters before standard handling by AbstractPlugin
TAS-468 updated ProjectionLoadPlugin to use a GenotypeTable data set from the Data Tree instead of requiring a input filename.
TAS-467 Changed cache size of HDF5ByteGenotypeCallTable. It was too high especially if the number of taxa is large and the max available heap size is relatively small.

New in TASSEL 5.0.9 (Feb 7, 2015)

TAS-465 Removed jar signing from build. Java Web Start is no longer supported.
TAS-446 Removing unused imports from GenomeFeatureMapBuilder
TAS-453 : replaced Taxon.getAnnotation() with Taxon.getTextAnnotation() to fix bug
TAS-472 : Fixed a bug in addTaxon() that caused a duplicate taxon in TAXA_ORDER when TAXA_ORDER not present
Moved to the call to createTaxaOrder(h5w) prior to the call to h5w.createGroup(path)
TAS-176 Implementation of GUI for full sib family imputation
TAS-474 Improvements to imputation of nucleotides
TAS-446 Trying to merge GenomeFeatureMap back into master
TAS-446 Added JSON library and functionality to build the directed graph holding GenomeFeature relations.
TAS-446 Added some of the export options
TAS-472 : added createTaxaOrder() for reverse compatibility
TAS-453 : Added a preferredHaplotypeSize parameter
TAS-468 Cleaned up ProjectionLoadPlugin to remove unused variables and obsolete comments.
TAS-446 Added JSON-reading capability and fixed location lookup ranges
removed instances of getGenotypeCopyInstance from FILLINImputationPlugin until speed fixed; fixed reporting for focus block viterbi in FILLINImputationPlugin
TAS-176 Initial (partial) implementation of the Plugin for FSFHap Imputation
TAS-429 debugged conversion to nucleotides and ported conversion method used for imputation paper to WritePopulationAlignment
TAS-94 Cleaned up HDF5Utils
TAS-94 Clean up HDF5ByteGenotypeCallTable
TAS-415 Add Support for PLink Files
TAS-429 Fixed bugs, made improvements, and added parameters for BiparentalHaplotypeFinder called by CallParentAlleles. This required new methods in HaplotypeCluster and HaplotypeClusterer.
TAS-455 Corrections to Projection CLI import (-projection)
TAS-468 Clean up ProjectionLoadPlugin
TAS-466 Added (incomplete) FilterGenotypeTableBuilder2
TAS-464 Fix so will output multiple phenotypes to distinct files.
TAS-464 Added functionality to CompressedMLMusingDoubleMatrix to export residuals to file (if option chosen)
TAS-446 Fixed location lookup on GenomeFeatureMapBuilder
added support for FILLIN accuracy by MAF to the plugin
TAS-453 : Complete first draft of this plugin (not tested yet)
TAS-461 added tests of additive and dominance effects to GLM
TAS-446 Minor tweaks to smooth out schema
TAS-446 Clean out old comments and stuff no longer needed
TAS-446 Changed schema for holding annotations; all now kept in a common (extensible) HashMap
TAS-40 Continued implementation of Site Scores based on Peter's suggestions.
Change TOGM format, adding PAV field
Modified setVariantDef() and setVariantPosOff() so that they work with ragged arrays
TAS-446 Added some validation for entered data
TAS-446 Progress update (adding imports, expanding methods; not functional yet, thought)
changes made to FSFHap to correct bug in code that filters out sites within tags and to allow processing of multiple genotype files at once so that the -separate command can be used with CallParentAlleles plugin.
TAS-455 Add import of Projection Genotype Table to Pipeline (CLI)
TAS-454 Changed GenotypeCallTableBuilder.getInstanceCopy() method to use Futures for multi-threading to avoid TimeoutException.
TAS-453 : still a work in progress
Added new restriction enzyme KpnI
Stub created for this new plugin
Part of the Automated Production Pipeline
TAS-427 Added function to get Position List from Genotype Table and make it a stand alone data set on the Data Tree.
TAS-452 Corrected DynamicBitStorage to wrap bit sets in UnmodifiableBitSets to make GenotypeTable instances unmodifiable in general.
fixed bug. Removed cast of GenotypeTable returned by FilterGenotypeTable.getInstance to FilterGenotypeTable, since the function sometimes returns a CoreGenotypeTable.
Removed most of the nano timers, except for the most pertinent ones
TAS-371 : ProductionSNPCallerPlugin now adds all taxa annotations present in the key file
fixed bug in permutation code that occurred when the model contained both factors and covariates
TAS-446 Ported Eli's Graph structures to branch
Added modeltype to command line parameters for StepwiseOLSModelFitterPlugin
TAS-391 Initial stubs and libraries for using BerkeleyDB
TAS-427 Added function to get Taxa List from Genotype Table and make it a stand alone data set on the Data Tree.
Added depth first search traversal for Graph
Updated size() methods for weighted edges
implement maxHetDev option setting so that junit test runs successfully
Adding directed graph with appropriate utilities with the builder
Adding basic graph utilities
Revert "Adding basic graph utilities"
This reverts commit 75fb45b787386357bd8e4e27b3a28aeb126c9d7e.
Adding basic graph utilities
TAS-445 fixes row method in EJMLDoubleMatrix and makes sure that row and column methods return column vectors
TAS-447 Created SiteNamesAvailableListModel to easily instantiate AbstractAvailableListModel for PositionList
TAS-447 Created TaxaAvailableListModel to easily instantiate AbstractAvailableListModel for TaxaList
TAS-448 Create HDF5 Schema Viewer
TAS-404 : fixed a bug in readTaxaAnnotationFile() related to parsing headers for quantitative annotations
They can start with "#" or "

New in TASSEL 5.0.8 (Feb 7, 2015)

TAS-398 Added option to TASSEL GUI that redirects logging messages to a window where the user can see logging messages.
TAS-429 made changes to parameters. made BiparentalHaplotypeCaller the default method
TAS-404 One step TBT parallelization concepts and initial implementation
TAS-40 Added Dosage to GenotypeTableBuilder
TAS-435 Added a few words to info message about not finding TasselBlas to clarify
TAS-429 Haplotype clustering changes used by BiparentalHaplotypeFinder
TAS-429 added new -cluster method to improve performance for S1's and residual heterozygosity. This replaces the old cluster method which did not perform will with few generations of selfing
modified getUsage to provide additional info about about parameters
TAS-398 Added -debug flag to Tassel Pipeline to set logging level to debug.
TAS-433 Changed action of pop up menu over Sequence Viewer. Before had to hold mouse button to keep menu visible. Now stays until you click again.
TAS-40 Changed Dosage to return byte since higher value integers can't be stored anyway.
TAS-40 Added Dosage class to site score package.
TAS-431 Remove class NucleotideGenotypeTable
TAS-40 Continued implementation of SiteScores. Added AlleleDepth which will be a replacement for net.maizegenetics.dna.snp.depth
TAS-40 Created SiteScore classes for ImputeProbability
TAS-40 Integrating AlleleProbabilityBuilder with GenotypeTableBuilder
TAS-389 added javadoc comments for GenotypePhenotype and its builder
TAS-389 added GenotypePhenotype and GenotypePhenotypeBuilder classes. GenotypePhenotype will replace both MarkerPhenotype and MarkerPhenotypeAdapter.
TAS-389 Moved TableReport implements to Phenotype interface
added CompareAlignments (deprecated) back into FILLINImputationAccuracy
Added restriction enzyme NspI
TAS-424 PluginParameters Enabled/Disabled Depending on value of another PluginParameter
TAS-40 Continued implementation of Site Scores
TAS-105 Changed command line flag from hetThresh to mxHet in FILLINImputationPlugin. Seems that is what it was since the test case uses it that way?
TAS-419 Changed javadoc index.html title to TASSEL 5.0: JavaDoc
added DEFAULT_NAME to TaxaAttribute
Corrected HetsToUnknownPlugin.getIcon() method
TAS-419 Changed javadoc index.html title to TASSEL JavaDoc API 5.0 (${build-date})
TAS-221 Create public static GenotypeCallTableBuilder getHomozygousInstance(GenotypeCallTable genotype) {
TAS-425 Refactor GenotypeTableBuilder.copyGenotypeInstance() to use GenotypeCallTableBuilder.getInstanceCopy()
Corrected SortGenotypeFilePlugin.getIcon() method.
TAS-378 Continued implementation of CombineGenotypeTable
TAS-389 debug changes made to pass current version of junit tests.
TAS-189 Handle negative values as double parameters for command line options
Improved Data Menu icons
Improved Load File icon
TAS-416 Added icon for SortGenotypeFilePlugin
TAS-426 Added SortGenotypeFilePlugin to Data Menu
FILLINFindHaplotypes -maxOutMiss parameter typo
FILLINFindHaplotypes functional
TAS-40 Added SiteScoreBuilder.getFilteredInstance()
TAS-40 Fixed byteToFloatPercentage(). It was returning 0's for all values.
TAS-389 Finished implementing FilterPhenotype.
finished implementing phenotype join methods in PhenotypeBuilder
TAS-105 Changed order of FILLIN plugins to have first used to be first on menu.
TAS-105 Created Impute menu on Tassel GUI for FILLIN and future imputation methods.
GUI support for FILLIN
Implementing Phenotype merging in PhenotypeBuilder. In progress.
TAS-105 Added FILLINFindHaplotypesPlugin to Tassel Data Menu
TAS-105 Added FILLINImputationPlugin to Tassel Data Menu
TAS-408 Add asterisk to required Plugin Parameters in Dialog
TAS-336 Better handling of PluginParameter verification checks.
TAS-40 Continued implementation of Site Scores
TAS-421 Change GenotypeCallTableBuilder.setBaseRangeForTaxon() implementation to use arraycopy()
TAS-398 Added utilities for setting logging level to DEBUG
TAS-163 Corrected implementation of FilterGenotypeTable.alleleDefinitions()
TAS-418 Corrected calls to siteOfPhysicalPosition() in FilterAlignmentPlugin to pass in first chromosome. In the past, null input meant to use first chromosome. In these situations in FilterAlgnmentPlugin, there are only one chromosome when filtering on position.
TAS-404 Concurrent version of DiscoveryPlugin
TAS-404 Changed new HashMap to new HashMap
TAS-404 Continued progress on one step TBT - parallelization
TAS-404 Expanding the annotation so that a key file can be processed as annotated taxa list
TAS-420 Add Glob support to DirectoryCrawler
TAS-418 Corrected call to siteOfPhysicalPosition() in FilterAlignmentPlugin to pass in Chromosome instead of null.
TAS-410 Improve parameter checking in DiscoverySNPCallerPlugin
TAS-399 Added code to generate runPlugin convenience method in Plugins
TAS-404 Improved documentation for TBT one step process
TAS 335 : Converted to new PluginParameter design
TAS-416 Added SortGenotypeFilePlugin (with minor changes to BuilderFromHapmap/FromVCF)
TAS-389 Changes made to implement filtering in PhenotypeBuilder
TAS-333 : Converted AddReferenceAlleleToHDF5Plugin to new PluginParameter design

New in TASSEL 5.0.7 (Feb 7, 2015)

TAS-389 Finished implementing file imports for PhenotypeBuilder
TAS-403 Convert ModifyTBTHDF5Plugin to new Plugin Parameter Design
TAS-40 Abstracted data storage from Allele Depth module and created new package net.maizegenetics.dna.snp.byte3d. Started implementation of Site Scores using byte3d as data storage.
TAS-103 Updated ProductionPipeline to use recent improvements to Plugin Parameter design.
Implementing file import methods
TAS-331 Initial implementation of FilterGenotypeTableBuilder.
Clean up allele depth classes.
TAS-392 : Now uses File.getName() or File.getCanonicalFile.getParent() to retrieve file names or parent directory
Instead of using substring on the String version of the file path.
TAS-411 Convert ProductionSNPCallerPlugin to new Plugin Parameter Design
TAS-410 Convert DiscoverySNPCallerPlugin to new Plugin Parameter Design
TAS-398 Convert Tassel Pipeline, Production Pipeline, and Tassel Main App to use new Logging Utilities.
TAS-398 Added new utilities class for logging.
TAS-412 Added HDF5SummaryPlugin to get summary data from HDF5 files (fixed typo of duplicate option flags)
TAS-412 Minor fix to HDF5SummaryPlugin to remove performFunction() method
TAS-412 Added HDF5SummaryPlugin to get summary data from HDF5 files
remove try {} for debugging in PanA
set multiple threading in PanA
Position block bug fixed in PanA
TAS-407 Adjusted layout of UNEAK and GBS menus
TAS-397 Add Tool Tip to Plugin Parameter Dialogs
TAS-407 Add UNEAK Menu to GUI
TAS-406 Updated UNEAK plugins to use the new PluginParameter functionality
TAS-405 Fix ExportUtils.WriteToVCF so it just outputs a summary of sites with no alleles.
TAS-375 Added javadoc to BinaryToTextPlugin getters and setters
TAS-396 Convert SeqToTBTHDF5Plugin to new Plugin Parameter Design
TAS-391 In Utils.getBufferedReader(), set buffer size of gzip stream also to specified buffer size.
TAS-336 Added verification that inFile() is a file (i.e. not a directory).
TAS-399 Create Code Generator for Plugin Parameter Getters and Setters
TAS-394 Added method for Parameter Plugin Description
Added restriction enzymes NlaIII and SphI
TAS-333 : Added some feedback on progress
TAS-390 Convert SAMConverterPlugin to new Plugin Parameter Design
TAS-336 Added Help Tab to Automatically generated dialogs for PluginParameters.
TAS-203 Improved documentation
TAS-393 PluginParameters now check that command-line names are unique
TAS-336 Added getParameterFields() method to AbstractPlugin.
TAS-389 Partial implementation of PhenotypeBuilder
TAS-391 - Stub with todos for the revision of fast parallel fastq reader
various bugs fixed to get the basic import test running.
Add PanAReadToKmerPlugin and a few bug fixes in PanA
TAS-389 partial implementation of PhenotypeBuilder with modifications to Categorical Attribute.
TAS-387 Convert TagCountToFastqPlugin to new Plugin Parameter Design
TAS-336 Improved AbstractPlugin verifying of Parameters using isEmpty() method.
TAS-336 Added method AbstractPlugin.postProcessParameters() to allow extending Plugins to modify / verify Parameters after user input and before processData().
TAS-356 Added code to AbstractPlugin that only prints out any given citation once.
TAS-203 Fixed imports that included Java 8
TAS-203 Adding tag direction reads and taxaList support to TBT module
TAS-336 Added isEmpty() method to PluginParameter
TAS-382 Changed labels on Manhattan and QQ Plots to say Log10 instead of just Log.
TAS-203 Beginning to implement HDF5 TBT following the builders and allowing for greater depth
Implement phenotype package classes and add PhenotypeBuilder
Implement phenotype package classes, add new FilterPhenotype class, delete ImportPhenotypeUtils
remove TagHDF5 interface
new version of CorePhenotype
make many changes to Phenotype implementation
TAS-380 Converted MergeMultipleTagCountsPlugin to Plugin Parameter Design
TAS-375 Minor modifications to setters/getters of BinaryToTextPlugin
TAS-340 Removed unneeded comments in Position
TAS-340 Removed unused import from WHICH_ALLELE
TAS-340 Fusion of Position.Allele with WHICH_ALLELE
TAS-340 Move Which_Allele upto DNA and add ancestral allele
TAS-377 Added builder like methods to FastqToTagCountPlugin
added AbstractPhenotype as the superclass of CorePhenotype and FilterPhenotype
TAS-377 Converted FastqToTagCountPlugin to new Plugin Parameter Design
change Phenotype to interface implemented by CorePhenotype and FilterPhenotype
TAS-378 Implement some methods in CombineGenotypeTable
TAS-336 Added validity check for IN_DIR and OUT_DIR to PluginParameter. Also added File Choosers that allow on directories to be chosen.
added TaxaAttribute and other implementation details
TAS-336 Added IN_DIR and OUT_DIR as possible file types in PluginParameter
TAS-336 Changed getter methods of BinaryToTextPlugin to return BinaryToTextPlugin instead of Plugin. This is so casting not needed when stringing calls together.
initial implementation of Phenotype objects
TAS-375 Removed Enum from BinaryToTextPlugin and changed command line flags to original for compatibility.
TAS-336 Moved all logic for checking Range inside PluginParameter.
TAS-303 HapMap reader that throws error messages with the row of bad data
TAS-160 Add ancestral, major, minor, and reference support to HDF5 position lists.
TAS-336 Added methods to Plugin to make defining Enum of PluginParameters optional.
Fixed PanAUsageExample.java
TAS-346 - FILLIN GUI removed as it is being supplanted by new plugin system
TAS-355 - Fixes pair site ordering incorrect HapMap must be ordered by position
PanA code completed.
TAS-132 : IBSDistanceMatrix is not using start & endword consistently - shifted to first and last word
Tools to ignore depth of coverage when converting from VCF to HDF5
TAS-336 Improved AbstractPlugin.getParameterInstance() to return null if not found. This allows for a better error message.
TAS-336 Added PluginParameter.Builder construction that takes String in addition to Enum
TAS-368 Improvements to plugin that lists all plugins.
TAS-374 Add UNEAK to TASSEL5 GBS - Code from Jason
TAS-368 Initial attempt at plugin that lists all plugins.
TAS-336 Changed AbstractPlugin.printParameterValues() to do nothing if no parameters.
TAS-375 Convert BinaryToTextPlugin to new Plugin Parameter Design
TAS-336 Migrating new Parameter Plugin design into the main code base.
Pick up training data set, transform with boxcox, convert to arff. PanA Start M5 training
TAS-367 : replaced System.out.println() calls with myLogger.info() or myLogger.error()

New in TASSEL 5.0.6 (Feb 7, 2015)

TAS-103 Added check to prevent exception in Production Pipeline in case usage statement is desired.
TAS-103 Additional modifications to logging of Production Pipeline
TAS-103 More adjustments to logging for the Production Pipeline.
TAS-103 Corrected logging of Production Pipeline.
TAS-103 Improved logging of Production Pipeline to send stdout, stderr, and log4j into same file.
TAS-315 Final bug found in VCF to HDF5 conversion
TAS-103 Added logging statement to ProductionPipeline to put arguments passed to ProductionSNPCallerPlugin into the log.
TAS-103 Rewrote ProductionPipeline using new Plugin Parameter Design. Code is much shorter and simpler.
Adding alignments from TOPMV3 to TagGWASMap
TAS-336 Added New BinaryToTextPlugin to GUI under new GBS Menu
TAS-336 Make printParameterValues() protected so that plugins that extend can call that.
TAS-103 Continue simplification of Production Pipeline
made rawSeqFileNameRegex public static final and removed rawSeqFileNameReplaceRegex
Modified clearVariants() and clearVariant() so that they work with ragged arrays
Fixed getVariantOff() so that it works with ragged arrays (additional change)
TAS-363 Added synchronized statements to addTaxa() and addSite() methods to prevent race condition.
Fixed getVariantOff() so that it works with ragged arrays
Added ".topm" as an acceptable suffix for a binary TOPM in writeTOPM()
1. Reformat tag GWAS mapping result to HDF5 2. Align tags in mapping result using Bowtie2 --very-sensitive-local -k 2 option 3. Add alignments into TOPMV3 (Multiple alignment topm), which is easier to identify unique ref tags for model training
Plugins of tag genetic mapping
TAS-362 Fix in GenotypeTableBuilder that sorts genotypes when it sorts the positions.
TAS-336 Added class BinaryToTextPluginNew which I migrated BinaryToTextPlugin to use the new Parameter Plugin design.
TAS-336 Improved Tassel Pipeline it accept either of these Plugin constructors Plugin(Frame) or Plugin(Frame, boolean). That way if Plugin used in GUI and CLI, only Plugin(Frame, boolean) needs to be implemented.
TAS-336 Plugin Parameters Design. Added code to create JComboBox if parameter is type Enum. Also added code to handle parameter default value vs required.
TAS-336 Added code to Plugin Parameter Concept to check that directory of output files exist.
modified -extOut in FILLINFindHaplotypes to include chromosome number and start/end positions
added a feature for FILLINFindHaplotypes to output which taxa go into which haplotype (using flag -extOut)
Genetic mapping code log update
TAS-336 Added code for better validating plugin parameters.
TAS-336 Continued development of auto-generating GUI for Plugin Parameter Concept.
TAS-336 Added code to Parameter Plugin Concept to handle clicking "Cancel"
TAS-336 Added code to Plugin Parameter Concept that automatically generates GUI for entering parameter values.
TAS-315 Create memory efficient VCF to HDF5 conversion nearly functional
Get block position from TOPM SimpleGenotypeSBit deflation set to 1
TAS-315 Create memory efficient VCF to HDF5 insert part 2
TAS-355 Added code to PositionListBuilder.validateOrdering() to print out two positions that are out of order.
TAS-354 Changed Tassel Pipeline flag from -mergeAlignments to -mergeGenotypeTables
TAS-354 Changed Menu and tool tip name from "Merge Alignments" to "Merge Genotype Tables"
TAS-354 Renamed MergeAlignmentsPlugin to MergeGenotypeTablesPlugin
TAS-336 Continued implementation of PluginParameter concept.
TAS-352 Add code to FileLoadPlugin to invoke reading FASTA files.
TAS-352 Added support for loading FASTA files
TAS-351 Corrected problem loading Phylip files
TAS-336 Proposed solution to one step to get parameter value for Plugins.
TAS-336 Continue implementing ParameterConceptPlugin
TAS-349 Fixed operation of Cancel button on Kinship Dialog
TAS-336 In ParameterConceptPlugin changed getParameterValue() to getParameter(). This will go in AbstractPlugin once this design is finished. Added main() to illustrate how Plugin can be setup with a Builder style method calls.
added support for anonymous haplotype naming in FILLINFindHaplotypesPlugin
added support for anonymous haplotype naming in FILLINFindHaplotypesPlugin
TAS-336 Implementing getParameterValue() and setParameterValue() for PluginParameter
TAS-326 and TAS-345. Also added an error IOException for when the output file (-o) in FILLINFindHaplotypesPlugin does not include gX
TAS-326 and TAS-345. Also added an error IOException for when the output file (-o) in FILLINFindHaplotypesPlugin does not include gX
TAS-336 Added Range checks for PluginParameter
TAS-336 Continued implementation of PluginParameter concept.
TAS-342 Added code to retain current view of TableReports which clicking between other data tree nodes.
TAS-341 Migrate MergeAlignmentsPlugin to Tassel 5. Written by Jason
TAS-334 Added ability to Data Tree to show text and graphical view of TOPM
TAS-169 Removed unused code from GenotypeSummaryPlugin
TAS-315 Minor progress towards create memory efficient VCF to HDF5
TAS-334 Initial implementation of Graphical TOPM Viewer
TAS-333 : Improvements to GeneralPosition Builder
Minor changes to the genomeVersion reporting when writePositions is true
TAS-315 Beginning of a more efficient VCF to H5 converter.
TAS-333 : Lots of changes so that adding the reference allele to an HDF5 genotype table will work "right"
I ran existing unit tests where possible and they all passed. If I messed something up, we can always revert. This is an initial stab at this which could be refined in many ways. For example, population of a PositionList with reference alleles should probably be moved to a PositionListUtils class.
moved methods in FILLINImputationAccuracy to a subclass
TAS-336 Plugin parameter concepts highlighted for everyone
TAS-335 : Simple plugin to split an HDF5 GenotypeTable by chromosome
TAS-333 : Minor change: System.out.println()'s of the updated positions is now optional (hard coded to no output)
These were for debugging/checking
TAS-322 : changed GeneralPosition to Position when comparing PositionLists (better style?)
TAS-333 : Now populates the global minor allele
This new plugin is nearly ready
TAS-324 Removed enum type FileLoadPlugin.TasselFileType.Numerical. FileLoadPlugin.TasselFileType.Phenotype is the new and preference file format.
TAS-322 : Added dash missing from line myArgsEngine.add("-iD", "--ignore-depth", false);
LDResult class is expanded to permit passing around LDResults for other analyses
Should provide a robust mechanism for only retaining the most significant results.
TAS-322 : Added an ignoreDepth (-iD) option to the MergeHDF5GenotypesSameSitesPlugin, as well as more efficient reading of positions to confirm that they match.
TAS-322 : Plugin to merge multiple HDF5 GenotypeTables containing the exact same sites
TAS-323 - Added public static FilterGenotypeTable getInstance(GenotypeTable a, PositionList subPositionList)
Added " sec" to all the nanosecond timer System.outs
Fixed bug which slowed down writing depths to HDF5 GenotypeTable
TAS-316: LibraryPrepID's can now be alphanumeric (i.e., Strings) OR integers. Stricter checking that the order of the columns is correct.
Added GenotypeTableBuilder.getTaxaIncrementalWithMerging(myTargetHDF5file, myPositionList, genoMergeRule)
So that a new hdf5 geno file can be created to which replicate taxa (from different flowcell_lanes in the same ProductionSNPCallerPlugin run) can be added & merged

New in TASSEL 5.0.5 (Feb 7, 2015)