All Classes Interface Summary Class Summary Enum Summary
| Class |
Description |
| AbstractDialogFactory<T extends Dialog> |
A factory responsible for building Dialogs from a supplied YAML file. |
| AbstractListBean |
Implements ListModel event listening funtionality
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| AdjustedGORLine |
|
| AdjustedGORLineIterator |
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| Argument |
A base class for all arguments.
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| ArgumentBuilder |
Base class for all argument builders.
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| ArgumentContent |
Class for perspective dialog argument content.
|
| ArgumentContent.Format |
Definition of argument content formats.
|
| ArgumentDescription |
Argument description class.
|
| ArgumentType |
Enumeration of argument types.
|
| BaseStreamIterator |
Iterator that is based on stream coming from the Supplier provided.
|
| BasicBean |
Bean that provides basic support for Java beans.
|
| BatchedPipeStepIteratorAdaptor |
Created by sigmar on 05/05/2017.
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| BatchedReadSource |
A wrapper rowSource reading the child rowSource in a thread into a buffer and offering to the main thread in batches
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| BatchedReadSourceConfig |
Created by sigmar on 26/04/2017.
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| BucketCreator<T extends org.gorpipe.gor.table.BucketableTableEntry> |
Helper class to create bucket files from bucket descriptions.
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| BucketCreatorGorPipe<T extends org.gorpipe.gor.table.BucketableTableEntry> |
Helper class to create bucket file from bucket description.
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| BucketManager<T extends org.gorpipe.gor.table.BucketableTableEntry> |
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| BucketManager.BucketPackLevel |
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| BucketManager.Builder<T extends org.gorpipe.gor.table.BucketableTableEntry> |
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| CalcCompiler |
CalcCompiler implements an Antlr parse tree visitor, starting on an expression node.
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| CalcLambdaBoolean |
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| CalcLambdaDouble |
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| CalcLambdaDoubleConstant |
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| CalcLambdaInteger |
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| CalcLambdaIntegerConstant |
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| CalcLambdaLong |
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| CalcLambdaLongConstant |
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| CalcLambdaNumeric |
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| CalcLambdaString |
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| CalcLambdaStringConstant |
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| CalcLambdaVariable |
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| ChartDataType |
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| ColumnGroup |
Holds a definition of columns that should be grouped together.
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| CombinationIterator |
Iterate through all combinations (n choose k) and provide permutations representing the combinations.
|
| Constant |
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| CvpBooleanLambda |
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| CvpDoubleLambda |
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| CvpIntegerLambda |
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| CvpLongLambda |
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| CvpStringLambda |
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| DateArgument |
Represents an argument that expects a date value.
|
| DateArgumentBuilder |
Responsible for building date arguments.
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| Dialog |
A basic dialog implementation
|
| DialogArgumentWrapper |
A wrapper for dialog arguments.
|
| DialogDescription |
Class for describing a dialog.
|
| DialogType |
The types of dialogs currently supported
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| DominantLogLikelihood |
Log likelihood calculator for dominant variant association.
|
| FileArgument |
Represents an argument that expects a file path.
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| FileArgumentBuilder |
Responsible for building file arguments.
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| FilteringColumnDefinition |
Interface for filtering column definition.
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| FreemarkerQueryUtilities |
Helper functions to parse and create reports with the freemarker parsing engine.
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| FreemarkerReportBuilder |
Report builder class for building freemarker based reports via yml files.
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| GavaLogLikelihood |
Log-likelihood ratio calculator for variant association.
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| GBasicRulesCalculator |
Checks the correctness of phase of haplotypes/genotypes using basic rules.
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| GChiSquared2by2 |
Chi-squared for 2-by-2 contingency tables.
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| GenericGorRunner |
This class handles the most basic gor pipe execution.
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| GenericRunnerFactory |
Factory method for creating an instance of the GenericGorRunner class.
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| GenericSessionFactory |
Factory class for creating default/generic gor sessions.
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| GenotypeLookupUtilities |
Genotype lookup utilities for generating vcf files from horizontal got gt data
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| GFisherExact2by2 |
Fisher's exact test for 2-by-2 tables.
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| GLogGamma |
Compute the log of the Gamma-function for integer values, i.e.,
compute log(n!) for n = 0,1,2,...
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| GorConstants |
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| GorJavaUtilities |
Created by sigmar on 21/12/15.
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| GorJavaUtilities.CmdParams |
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| GorJavaUtilities.PhenoInfo |
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| GorJavaUtilities.Phenotypes |
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| GorJavaUtilities.PRPRPRValue |
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| GorJavaUtilities.PRPRValue |
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| GorJavaUtilities.VCFValue |
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| GORLine |
This class merges gor lines from multiple BufferedReaders.
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| GorParquetFileOut |
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| GorParquetWriter |
Writes parquet file from a stream of gor/nor rows
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| GorParquetWriter.GorParquetBuilder |
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| GorParquetWriteSupport |
Translates a gor/nor row to corresponding format in a parquet file
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| GorParsingError |
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| GorRowFilterFunction<T extends org.gorpipe.gor.model.Row> |
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| GorRowInferFunction |
For map-reduce type inferance, such as in SparkSQL which needs a schema
The gor type syntax, I for Int, D for Double and S for String
Two rows with types I and S are reduced to type S etc.
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| GorRowMapFunction |
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| GorRowQueryFunction |
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| GorScriptAnalyzer |
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| GorScriptBaseListener |
This class provides an empty implementation of GorScriptListener,
which can be extended to create a listener which only needs to handle a subset
of the available methods. |
| GorScriptBaseVisitor<T> |
This class provides an empty implementation of GorScriptVisitor,
which can be extended to create a visitor which only needs to handle a subset
of the available methods. |
| GorScriptLexer |
|
| GorScriptListener |
This interface defines a complete listener for a parse tree produced by
GorScriptParser. |
| GorScriptParser |
|
| GorScriptParser.ArgumentContext |
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| GorScriptParser.Calc_commandContext |
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| GorScriptParser.Calc_expression_listContext |
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| GorScriptParser.Calc_expressionContext |
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| GorScriptParser.Column_listContext |
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| GorScriptParser.Column_nameContext |
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| GorScriptParser.Column_numberContext |
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| GorScriptParser.Column_rangeContext |
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| GorScriptParser.Column_refContext |
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| GorScriptParser.Column_rename_ruleContext |
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| GorScriptParser.Column_selectionContext |
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| GorScriptParser.Column_wildcardContext |
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| GorScriptParser.Compare_expressionsContext |
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| GorScriptParser.Create_statementContext |
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| GorScriptParser.Def_macroContext |
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| GorScriptParser.ExpressionContext |
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| GorScriptParser.FactorContext |
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| GorScriptParser.FilenameContext |
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| GorScriptParser.Function_callContext |
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| GorScriptParser.Function_exprContext |
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| GorScriptParser.Function_nameContext |
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| GorScriptParser.Generic_commandContext |
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| GorScriptParser.Gor_expressionContext |
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| GorScriptParser.Gornor_expressionContext |
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| GorScriptParser.Hide_commandContext |
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| GorScriptParser.If_exprContext |
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| GorScriptParser.In_expressionContext |
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| GorScriptParser.Indag_expressionContext |
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| GorScriptParser.Input_sourceContext |
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| GorScriptParser.Macro_nameContext |
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| GorScriptParser.Macro_valueContext |
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| GorScriptParser.Nested_queryContext |
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| GorScriptParser.Nor_expressionContext |
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| GorScriptParser.Not_rel_exprContext |
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| GorScriptParser.NumberContext |
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| GorScriptParser.Option_valueContext |
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| GorScriptParser.Optional_power_factorContext |
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| GorScriptParser.OptionContext |
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| GorScriptParser.Options_and_argsContext |
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| GorScriptParser.Paren_exprContext |
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| GorScriptParser.Paren_rel_exprContext |
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| GorScriptParser.Pgor_expressionContext |
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| GorScriptParser.Pipe_commandContext |
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| GorScriptParser.Power_factorContext |
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| GorScriptParser.Predicate_factorContext |
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| GorScriptParser.PredicateContext |
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| GorScriptParser.Query_expressionContext |
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| GorScriptParser.Rel_exprContext |
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| GorScriptParser.Rel_termContext |
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| GorScriptParser.Rename_commandContext |
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| GorScriptParser.Replace_commandContext |
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| GorScriptParser.ScriptContext |
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| GorScriptParser.Select_commandContext |
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| GorScriptParser.Signed_factorContext |
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| GorScriptParser.String_literal_listContext |
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| GorScriptParser.String_literalContext |
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| GorScriptParser.TermContext |
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| GorScriptParser.ValueContext |
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| GorScriptParser.VariableContext |
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| GorScriptParser.Virtual_relation_nameContext |
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| GorScriptParser.Virtual_relationContext |
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| GorScriptParser.Where_commandContext |
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| GorScriptParser.XfactorContext |
|
| GorScriptVisitor<T> |
This interface defines a complete generic visitor for a parse tree produced
by GorScriptParser. |
| GorSessionCacheManager |
Class that stores the session cache on a requestId key.
|
| GorSessionFactory |
|
| GorStreamIterator |
|
| GPParser |
Utility functions for parsing genotype probability triplets.
|
| GridArgument |
Argument for selecting grids or values from grids.
|
| GridArgumentBuilder |
Builder for grid argument.
|
| GTGen |
A class for running simple joint variant calling.
|
| HeaderCVP |
|
| IOTestAnalyser |
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| LinearAlgebra |
|
| LinearRegression |
|
| ListRowAdaptor |
|
| LocalFileCacheClient |
Local implementation of file cache client working directly against the file system.
|
| LogisticRegression |
This program fits a logistic regression model on a given data set.
|
| MathArrayUtils |
Provides various useful functions on arrays.
|
| NetworkTemplateLoader |
|
| NoCacheFileCacheClient |
Stub implememntation of FileCache, that doesn't do any caching - for running with caching disabled.
|
| NordIterator |
Iterator to access data from a nor dictionary file.
|
| NordIteratorEntry |
|
| NorStreamIterator |
|
| NorToGorPipeStep |
Created by sigmar on 16/08/2016.
|
| NumberArgument |
Represents an argument that expects a numeric value.
|
| NumberArgumentBuilder |
Responsible for building number arguments.
|
| OptionEvaluator |
|
| ParallelExecutor |
This class encapsulates a general execution in parallel of the pgor command when a
standard parallel query handler is not used.
|
| Perspective |
Represents a particular perspective onto data returned from a dialog query.
|
| Perspective.VIEW_TYPE |
Defines the type of view that should be selected by default when the perspective is activated.
|
| PerspectiveDialog |
|
| PerspectiveDialogDisplayParams |
Class for defining a perspective dialog display parameters.
|
| PerspectiveDialogFactory |
|
| PlinkAdjustAdaptor |
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
|
| PlinkAdjustment |
|
| PlinkArguments |
This class stores the phenotype file for plink vcf input header generation
Also the argument to the plink external process
|
| PlinkProcessAdaptor |
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
|
| PlinkVcfProcessAdaptor |
This analysis class collects gor or vcf lines and writes them in batches to a temporary vcf files read by plink2 process
|
| PowerLookupTable |
|
| ProcessIteratorAdaptor |
Created by sigmar on 03/11/15.
|
| ProcessRowSource |
Created by sigmar on 12/02/16.
|
| ProcessSource |
Created by sigmar on 12/02/16.
|
| QueryArgument |
Represents an argument that uses a gor/nor query to create the values the user can select from.
|
| QueryArgumentBuilder |
Responsible for building GOR/NOR query arguments.
|
| QueryEvalMethodModel |
|
| RangedNumberFormatter |
A number formatter that can constrain values to a minimum and/or maximum value.
|
| RecessiveLogLikelihood |
Log likelihood calculator for recessive variant association.
|
| RegularLogLikelihood |
Log likelihood calculator for regular variant association.
|
| ReportViewer |
Report container is implemented by viewmanagers that will display Reports created from Report Forms.
|
| RequestStats |
|
| RowBuffer |
An array of GOR row objects implementing iterator interface
The user class, BatchedReadSource, ensures thread safety
|
| SemanticChecker |
|
| SessionBasedQueryEvaluator |
|
| SigmoidFunction |
A class which uses a lookup table to compute the sigmoid function x -> 1/(1 + e^(-x)) up to a precision of 10^(-10).
|
| SkipFirstMethodModel |
Template model that enables template writer to skip first occurence of a given argument.
|
| StatisticalAdjustment |
|
| StringArgument |
Represents an argument that expects a string value.
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| StringArgumentBuilder |
Responsible for building string arguments.
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| SubjectLists |
Class holding information on lists and their content.
|
| SyntaxChecker |
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| TableManager |
Class to manage gor tables (dictionaries and tables).
|
| TableManager.Builder |
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| TypedCalcLambda |
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| ValueFormatter |
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| VariantAssociation |
Variant association algorithm, based on the VAAST algorithm.
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| VariantCounts |
|