Index (Eoulsan 2.6.1 API)

A B C D E F G H I J K L M N O P R S T U V W X Z
All Classes All Packages

A

ABORTED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
ABOUT_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: About string, plain text version.
AbstractAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an abstract Action
AbstractAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.AbstractAction
AbstractBAM2SAMModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define a module for converting BAM files into SAM.
AbstractBAM2SAMModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
AbstractClusterTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class is a scheduler for task running on a cluster.
AbstractClusterTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.AbstractClusterTaskScheduler
AbstractClusterTaskScheduler.ProcessThreadOutput - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class allow to fetch standard output or standard error.
AbstractConcatInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class define an InputStream that concatenate InputStream.
AbstractConcatInputStream() - Constructor for class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
AbstractEoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan: This class define an abstract EoulsanRuntime.
AbstractEoulsanRuntime(Settings) - Constructor for class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime
AbstractEoulsanRuntime.EoulsanExecMode - Enum in fr.ens.biologie.genomique.eoulsan: This Enum define the Eoulsan execution mode.
AbstractExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This class define an abstract executor interpreter that contains the default implementation of the execute() method that use a ProcessBuilder.
AbstractExecutorInterpreter() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter
AbstractExpressionModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression: This abstract class define and parse arguments for the expression module.
AbstractExpressionModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
AbstractFilterAndMapReadsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define an abstract module for read filtering, mapping and alignments filtering.
AbstractFilterAndMapReadsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
AbstractInfoAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an abstract action that show the some Eoulsan configuration and available modules
AbstractInfoAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
AbstractMetadata - Class in fr.ens.biologie.genomique.eoulsan.design: This abstract class defines methods for metadata.
AbstractMetadata() - Constructor for class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
AbstractModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define an abstract Module.
AbstractModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
AbstractParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define an abstract class for tool element parameters.
AbstractParameterToolElement(Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractParameterToolElement: Protected constructor.
AbstractPort - Class in fr.ens.biologie.genomique.eoulsan.core: Abstract class that define a port.
AbstractPorts<E extends Port> - Class in fr.ens.biologie.genomique.eoulsan.core: This class define a basic implementation of a Ports class.
AbstractPorts(Set<E>) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts: Constructor.
AbstractReadsFilterModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define an abstract module for read filtering.
AbstractReadsFilterModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
AbstractReadsMapperModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define an abstract module for read mapping.
AbstractReadsMapperModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
AbstractRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements: This class define an abstract requirement.
AbstractRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
AbstractResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util: This class define an abstract resource loader.
AbstractResourceLoader() - Constructor for class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader
AbstractRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r: This class define an abstract RExecutor.
AbstractRExecutor(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Constructor.
AbstractSAM2BAMModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define a module for converting SAM files into BAM.
AbstractSAM2BAMModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
AbstractSAM2FASTQModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define a module for converting SAM files into BAM.
AbstractSAM2FASTQModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
AbstractSAMFilterModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define an abstract module for alignments filtering.
AbstractSAMFilterModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
AbstractSplice2BEDModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping: This class define a module for converting SAM files into BED.
AbstractSplice2BEDModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
AbstractStep - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a step of the workflow.
AbstractTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class define an abstract task scheduler.
AbstractTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Protected constructor.
AbstractToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define an abstract tool element.
AbstractToolElement(Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Instantiates a new abstract tool element.
AbstractToolElement(Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Instantiates a new abstract tool element.
AbstractWorkflow - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a Workflow.
AbstractWorkflow(ExecutorArguments, Design) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Protected constructor.
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.eoulsan.ui.UIService
accept(Class<?>, boolean) - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Check that annotation of a class is compatible with the Eoulsan mode (local or Hadoop).
accept(Path) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.PrefixPathFilter
accept(Path) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils.SuffixPathFilter
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
action(List<String>) - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Execute action.
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
action(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
Action - Interface in fr.ens.biologie.genomique.eoulsan.actions: This interface define an action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.InfoAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction: Name of this action.
ActionService - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define a service to retrieve an Action
ActionService() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ActionService: Private constructor.
add(EmergencyStopTask) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks: Add an emergency task.
add(String, Object) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Store some data.
addBcl2FastqSamplesheetProject(SampleSheet, String, File) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add all the sample from a Bclfastq samplesheet.
addBcl2FastqSamplesheetProject(File, String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add all the samples from a Bcl2Fastq samplesheet.
addConstant(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Add a constant.
addConstant(String, String, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Add a constant.
addConstants(ExecutorArguments) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Add job arguments information to constants.
addDataToList(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
addDataToList(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
addDataToList(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Add a data to the list of data.
addDataToList(String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
addDataToList(String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
addDataToList(String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Add a data to the list of data.
addDependency(AbstractStep) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Add a dependency for this step.
addDependency(AbstractStep) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies: Add a dependency.
addDependency(StepInputPort, StepOutputPort) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Add a dependency for this step.
addExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Add an experiment.
addFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add a file to the design builder
addFile(File, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.JarRepack: Add a file to the jar file.
addFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add a filename to the design builder
addFiles(String[]) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add filenames to the design builder
addFiles(List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Add filenames to the design builder
addHadoopJobEmergencyStopTask(ClusterTaskScheduler, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask: Add a cluster Job to the EmergencyStopTasks.
addHadoopJobEmergencyStopTask(Job) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask: Add an Hadoop Job to the EmergencyStopTasks.
addHandler(Handler) - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler: Add an Handler.
ADDITIONAL_ANNOTATION_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
ADDITIONAL_ANNOTATION_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Additional annotation data format.
AdditionalAnnotationDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a additional annotation protocol.
AdditionalAnnotationDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
additionalScriptEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler: Define additional environment variable for bpipe scripts.
additionalScriptEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.HTCondorTaskScheduler
addObserver(StepObserver) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Add a listener.
addPort(String, boolean, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, boolean, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Add an output port.
addPort(String, boolean, DataFormat, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, boolean, DataFormat, CompressionType) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Add an output port.
addPort(String, boolean, DataFormat, EnumSet<CompressionType>) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, boolean, DataFormat, EnumSet<CompressionType>, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Add an output port.
addPort(String, DataFormat, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, DataFormat, CompressionType) - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Add an output port.
addPort(String, DataFormat, EnumSet<CompressionType>) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addPort(String, DataFormat, EnumSet<CompressionType>, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Add an input port.
addResource(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader: Add a resource.
addResourcePath(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Add a resource path.
addResourcePaths(Collection<String>) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Add a resource paths.
addResult(TaskContextImpl, TaskResultImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Add a task result to the step result.
addSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Add a sample.
addSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
addSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
addSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Add a sample.
afterExecute(Runnable, Throwable) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
afterExecuteTask(TaskContextImpl, TaskResultImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Set the state of the context after executing a task.
ALIGNMENTS_REJECTED_BY_FILTERS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
ALIGNMENTS_WITH_INVALID_SAM_FORMAT - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
ALIGNMENTS_WITH_MORE_ONE_HIT_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters
allPortsRequiredInWorkingDirectory(InputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Set all ports of an existing input ports to be required in working directory.
AMAZON - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
AMBIGUOUS_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
ANNOTATED_EXPRESSION_RESULTS_ODS - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: ODS Annotated expression results data format.
ANNOTATED_EXPRESSION_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: TSV Annotated expression results data format.
ANNOTATED_EXPRESSION_RESULTS_XLSX - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: XLSX Annotated expression results data format.
ANNOTATION_GFF - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: GFF data format.
ANNOTATION_GTF - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: GTF data format.
AnnotationDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a annotation protocol.
AnnotationDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
ANY_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock: The magic version number that allows any mutation to always succeed regardless of actual version number.
ApacheCommonCompressionCodecs - Class in fr.ens.biologie.genomique.eoulsan.io: This class allow to create input and output stream for compression codecs of the Apache Common Compression library.
ApacheCommonCompressionCodecs() - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs
APP_BUILD_COMMIT - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The built commit of the application.
APP_BUILD_DATE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The build date of the application.
APP_BUILD_HOST - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The built host of the application.
APP_BUILD_NUMBER - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The built number of the application.
APP_BUILD_YEAR - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The build year of the application.
APP_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The name of the application.
APP_NAME_LOWER_CASE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The name of the application.
APP_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The version of the application.
APP_VERSION_STRING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: The version of the application.
ASAP - fr.ens.biologie.genomique.eoulsan.core.Step.DiscardOutput
ASCII_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: Ascii charset.
ASCII_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.io.FileCharsets: Ascii file encoding.
ASCII_LETTER_OR_DIGIT - Static variable in class fr.ens.biologie.genomique.eoulsan.core.Naming
AVAILABLE_BINARY_ARCH - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Platforms where the application is available.
AVAILABLE_BINARY_ARCH_ALIAS - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Platforms alias.
AVAILABLE_PROCESSORS_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Available processor constant name.
AWS_S3_ACCESS_KEY_ID_PARAM_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
AWS_S3_SECRET_ACCESS_KEY_PARAM_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop

B

badParameterValue(StepConfigurationContext, Parameter, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for bad parameter value.
badParameterValue(String, Parameter, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Throw a exception for bad parameter value.
BAM2SAMLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This class define a module for converting BAM files into SAM.
BAM2SAMLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.BAM2SAMLocalModule
BAMMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a merger class for SAM files.
BAMMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
BAMSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a splitter class for BAM files.
BAMSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
base64ForIcon(String, Class) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCRuntimePatcher: This method replace the HTMLReportArchive.base64ForIcon() method.
BasicUI - Class in fr.ens.biologie.genomique.eoulsan.ui: This class define a basic UI for Eoulsan.
BasicUI() - Constructor for class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
BedToolsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling: This class uses tools from the BEDTools suite.
BedToolsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
beforeExecute(Thread, Runnable) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.PausableThreadPoolExecutor
beforeExecuteTask(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Set the state of the context before executing a task.
BIGBED - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BigBed format.
BIGWIG - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BigWig format.
BLIND - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod
BooleanParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a boolean tool element parameter.
BooleanParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement: Instantiates a new boolean tool parameter.
BooleanParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.BooleanParameterToolElement: Instantiates a new boolean tool parameter.
BOWTIE_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Bowtie index data format.
BOWTIE2_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Bowtie2 index data format.
BpipeTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class allow to submit, stop and get the status of jobs using Bpipe scheduler wrappers.
BpipeTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
BufferedHandler - Class in fr.ens.biologie.genomique.eoulsan: This class define a buffered handler.
BufferedHandler() - Constructor for class fr.ens.biologie.genomique.eoulsan.BufferedHandler
BUILD_CONTRAST_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
BUILD_DATE_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Build date constant name.
BUILD_NUMBER_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Build number constant name.
BundledScriptBpipeTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define an abstract scheduler that use a bpipe script bundled in Eoulsan distribution.
BundledScriptBpipeTaskScheduler(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler: Constructor.
BWA_INDEX_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: BWA index data format.
BYPASS_PLATFORM_CHECKING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Bypass platform checking.
ByteCountInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This filter class allow to count the number of bytes read by an inputStream.
ByteCountInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream: Public constructor
ByteCountInputStream(InputStream, long) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream: Public constructor
ByteCountOutputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class define a filter that count the number of written bytes by an InputStream.
ByteCountOutputStream(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream: Public constructor.
ByteCountOutputStream(OutputStream, long) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream: Public constructor.

C

CALL_METHOD - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter: The Constant CALL_METHOD.
canDelete() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the delete() method is available with this protocol.
canDelete() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canDelete() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
canList() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the list() method is available with this protocol.
canList() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canList() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
canMkdir() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the mkdir() and mkdirs() methods are available with this protocol.
canMkdir() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canMkdir() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
canonicalize() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
canRead() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if source is readable with this protocol.
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
canRead() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
canRename() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the renameTo() method is available with this protocol.
canRename() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canRename() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
canSymlink() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if the symlink() method is available with this protocol.
canSymlink() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canWrite() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test if source is writable with this protocol.
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
canWrite() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
changeFileExtension(File, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor: Change the extendsion of a file
check(Data, CheckStore) - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Launch the check.
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
check(Data, CheckStore) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
CHECK_COMPLETION_TIME - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
checkAnnotations(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Check if there is more than one annotation in the design
checkDirectories() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Check directories needed by the workflow.
Checker - Interface in fr.ens.biologie.genomique.eoulsan.checkers: This interface define a checker.
CHECKER_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
CheckerModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class is a module that launch checkers.
CheckerModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule: Public constructor.
checkExistingDirectoryFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a directory exists
checkExistingFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a file exists
checkExistingStandardFile(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a file exists
checkExistingStandardFileOrDirectory(Path, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Check if a file exists
checkExperimentDesign(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker: Check experiment design.
checkForPartDuplicates() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
checkForPartDuplicates() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
checkGenomes(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Check if there is more than one genome in the design
checkOutputSpecs(JobContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
checkRepTechGroupCoherence(List<String>, List<String>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Check if there is a problem in the repTechGroup coherence.
checkSamples(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Check if there are duplicate samples in the design.
CheckStore - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a storage where some results of the checker can be save for later reuse by other checkers.
CheetahInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: This class create a Cheetah interpreter, it can build a command line tool from command tag from Galaxy tool XML file.
CheetahInterpreter(String, Map<String, String>) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter: Instantiates a new tool Cheetah script interpreter.
ChIPSeqDataFormats - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq: This class contains the definition of some DataFormats for ChiP-Seq.
ClassLoaderObjectInputStream - Class in fr.ens.biologie.genomique.eoulsan.util: This class allow to use ObjectInputStream with a ClassLoader that is not the default bootstrap ClassLoader.
ClassLoaderObjectInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassLoaderObjectInputStream: Constructor, use the thread ClassLoader to load classes of objects to instantiate.
ClassLoaderObjectInputStream(ClassLoader, InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassLoaderObjectInputStream: Constructor.
ClassPathResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util: This class allow to define a resource loader for resources in the class path.
ClassPathResourceLoader(Class<S>, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.ClassPathResourceLoader: Constructor.
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.PreTreatmentExpressionMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PreTreatmentMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperMapper
cleanup(Mapper.Context) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterMapper
cleanupJob(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
cleanupJob(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Cleanup after a job.
clear() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Clear the content of the CheckStore.
clear() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Clear the entries of the object.
CLIMergingAnySAMOutputFormat<K> - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
CLIMergingAnySAMOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
close() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
close() - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
close() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.AbstractConcatInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.MaxByteInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterInputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
close() - Method in class fr.ens.biologie.genomique.eoulsan.util.JarRepack: Close the repackaged file.
close(JobContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils.SAMHeaderWriter: Close the SAM file header.
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionRecordWriter
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordWriter
close(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordWriter
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
closeConnection() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Close the connection.
closeConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
cloudInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with cloud configuration informations.
CLUSTER - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
CLUSTER_TASK - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
ClusterCombinedTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class defined a combined task scheduler for cluster mode.
ClusterCombinedTaskScheduler(int, ClusterTaskScheduler) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler: Constructor.
ClusterExecAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define the cluster exec Action.
ClusterExecAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
clusterInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with cluster configuration informations.
ClusterJobEmergencyStopTask - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define an EmergencyStopTask for cluster Jobs.
ClusterJobEmergencyStopTask(ClusterTaskScheduler, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask: Public constructor.
ClusterTaskAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define a action to launch a task on a cluster.
ClusterTaskAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
ClusterTaskScheduler - Interface in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This interface define a cluster task scheduler.
ClusterTaskScheduler.StatusResult - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a Status result return by the statusJob() method of the interface.
ClusterTaskScheduler.StatusValue - Enum in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This enum define the values of the status of a job.
ClusterTaskSchedulerService - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a service to retrieve a ClusterTaskScheduler.
CollectionUtils - Class in fr.ens.biologie.genomique.eoulsan.util: This class define an utility class that contains useful methods for collections.
CombinedTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers: This class defined a combined task scheduler that use several context schedulers according to the parallelization mode of the step.
CombinedTaskScheduler(int) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler: Constructor.
COMMA - Static variable in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: SPLITTER.
commandLineInfo(Main) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with command line informations.
CommandStep - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a step based on a Command object (workflow file).
CommandStep(AbstractWorkflow, Module) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow, Module, Set<Parameter>) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a step for a standard step from an existing step object.
CommandStep(AbstractWorkflow, Step.StepType) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Constructor that create a step with nothing to execute like ROOT_STEP, DESIGN_STEP and FIRST_STEP.
CommandStep(AbstractWorkflow, DataFormat) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a Generator Workflow step.
CommandStep(AbstractWorkflow, String, String, String, Set<Parameter>, boolean, Step.DiscardOutput, int, int, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a step for a standard step.
CommandStep(AbstractWorkflow, String, String, String, Set<Parameter>, boolean, Step.DiscardOutput, int, int, String, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandStep: Create a step for a standard step.
CommandWorkflow - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a workflow based on a Command object (workflow file).
CommandWorkflow(ExecutorArguments, CommandWorkflowModel, List<Module>, List<Module>, Design) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflow: Public constructor.
CommandWorkflowModel - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define the workflow model object of Eoulsan.
CommandWorkflowModel() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Public constructor.
CommandWorkflowModel(boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Public constructor.
CommandWorkflowParser - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class allow parse the workflow file.
CommandWorkflowParser(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Public constructor.
CommandWorkflowParser(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Public constructor.
CommandWorkflowParser(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Public constructor.
CommandWorkflowParser.StepOutputPort - Class in fr.ens.biologie.genomique.eoulsan.core.workflow
COMMENT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
Common - Class in fr.ens.biologie.genomique.eoulsan: This class define common constants.
CommonHadoop - Class in fr.ens.biologie.genomique.eoulsan: This class define common constants and other methods specific to Hadoop mode.
CommonHadoop() - Constructor for class fr.ens.biologie.genomique.eoulsan.CommonHadoop
compareTo(Parameter) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
compareTo(StepOutputDataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
compareTo(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
compareTo(DataFileDataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
compareTo(Ticket) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
COMPARISONS_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
compatibilityFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the filename using Eoulsan 1.x naming.
COMPLETE - fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusValue
CompressedSplitFastqLineReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop
CompressedSplitFastqLineReader(SplitCompressionInputStream, Configuration, byte[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
computeMD5Sum(DataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage
concat(List<Path>, Path, boolean, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy all files in a directory to one output file (merge).
concat(List<Path>, Path, boolean, boolean, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy all files in a directory to one output file (merge).
concat(List<Path>, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy all files in a directory to one output file (merge).
CONDITION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata
CONDITION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
ConditionalToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a conditional tool element.
ConditionalToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement: Instantiates a new tool conditional element.
conf - Variable in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
configure() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Set the parameters of the step to configure the module.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Set IDR parameters to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule: Set the parameters of the step to configure the step.
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
configure(StepConfigurationContext, Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
configure(Settings) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler
configure(Settings) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Configure the scheduler.
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Set the parameters of the checker to configure the checker.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Parse tool file to extract useful data to run tool.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: Configure the requirement.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Merger: Configure the merger.
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
configure(Set<Parameter>) - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
configure(Set<Parameter>) - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Splitter: Configure the splitter.
configureChecker(DataFormat, Set<Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule: This method allow to configure a checker from the configure method of other steps, that's why this method is static.
CONFIGURED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
configureLog4J(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.OtherLogConfigurator: Configure Log4J.
configureSampling(Path, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
CONTACT_EMAIL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Project email.
contains(E) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
contains(E) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Test if a port exists by testing if port name exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Test if a data exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
contains(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Test if a port exists.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
contains(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Test if the key is in md.
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
contains(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
containsAdditionalAnnotationFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Test if the additional annotation file field exists.
containsAdditionalAnnotationFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
containsBuildContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the buildContrast option exists.
containsBuildContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsComment() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the comment field exists.
containsComparisons() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the comparisons option exists.
containsComparisons() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Test if the condition field exists.
containsCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
containsCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the condition field exists.
containsCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
containsContrast() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the contrast option exists.
containsContrast() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsContrastFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the contrastFile option exists.
containsContrastFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsDate() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the date field exists.
containsDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the description field exists.
containsDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the designFile option exists.
containsDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Test if the experiment exists.
containsExperimentName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
containsFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the fastq format field exists.
containsGenomeFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Test if the genomeFile field exists.
containsGenomeFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
containsGffFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Test if the gffFile field exists.
containsGffFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
containsGtfFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Test if the gtfFile field exists.
containsGtfFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
containsKey(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Test if a key exists.
containsModel() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the model option exists.
containsModel() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsOperator() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the operator field exists.
containsParameter(Set<Parameter>, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: test if a set of parameters contains a parameter.
containsReads() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the reads field exists.
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the reference option exists.
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Test if the reference field exists.
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
containsReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the reference field exists.
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
containsReferenceField(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Test if an experiment contains reference fields
containsRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Test if the RepTechGroup field exists.
containsRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
containsRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the RepTechGroup field exists.
containsRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
containsSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Test if the experiment contains a sample.
containsSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
containsSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
containsSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Test if the sample exists.
containsSampleName(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design
containsSerialNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the serial number field exists.
containsSkip() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Test if the skip option exists.
containsSkip() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
containsUUID() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Test if the UUID field exists.
ContextUtil - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli: Utility methods to allow applications to deal with inconsistencies between MapReduce Context Objects API between hadoop-0.20 and later versions.
ContextUtil() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
ContextUtils - Class in fr.ens.biologie.genomique.eoulsan.core: This class define utility methods on Context.
CONTRAST_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
CONTRAST_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
convert() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter
convert(Configuration, DataFile, DataFile, DataFile, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq: Create the job to convert FASTQ files in a TFQ file.
convert(Configuration, Path, Path, Path, int) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq: Create the job to convert FASTQ files in a TFQ file.
copy(InputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Convenient method to create a defensive copy of an InputPorts object.
copy(OutputPorts) - Static method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Convenient method to create a defensive copy of an OutputPorts object.
copy(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFiles: Copy a file, if input data is compressed, data will be uncompressed and if output require to be compressed output will be compressed.
copy(DataPath) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HadoopUploadModule
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.LocalUploadModule
copy(Map<DataFile, DataFile>) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule: Copy files to destinations.
copy(Configuration, String, String, Path, boolean, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp: Deprecated.
copy(Path, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy file from a path to another path.
copy(Path, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy file from a path to another path.
copyAndCompressInputStreamToPath(InputStream, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy bytes from an InputStream to a path.
copyAndCompressLocalFileToPath(File, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a local file to a path
copyAndCompressLocalFileToPath(File, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a local file to a path
CopyDesignAndWorkflowFilesToOutputModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop: This module copy design and workflow file to output directory.
CopyDesignAndWorkflowFilesToOutputModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
copyFromPathToLocalFile(Path, File, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a file from a path to a local file
copyFromPathToLocalFile(Path, File, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a file from a path to a local file.
CopyInputDataModule - Class in fr.ens.biologie.genomique.eoulsan.modules: Copy input files of a format in another location or in different compression format.
CopyInputDataModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
copyInputStreamToPath(InputStream, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy bytes from an InputStream to a path.
copyLocalFileToPath(File, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a local file to a path
copyLocalFileToPath(File, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Copy a local file to a path
copyMerge(Path, Path, boolean, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Merge several file of a directory into one file.
copyMerge(Path, Path, boolean, Configuration, String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Merge several file of a directory into one file.
copyMerge(Path, Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Merge several file of a directory into one file.
CopyOutputDataModule - Class in fr.ens.biologie.genomique.eoulsan.modules: Copy output files of a step with a specified format to the output directory.
CopyOutputDataModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
copyTo(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Copy this DataFile in a other DataFile.
correctSAMRecordForMerging(SAMRecord, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils: Changes the given SAMRecord as appropriate for being placed in a file whose header is getSAMHeaderMerger(conf).getMergedHeader().
count(ExpressionCounter, DataFile, ReporterIncrementer, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterUtils: Count the the features.
countDataFormat(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
countDataFormat(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Count the number of occurrences of a format in the port.
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Group for hadoop counters.
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
COUNTER_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
COUNTER_GROUP_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.CommonHadoop
COUNTER_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
counterName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Get the name of the counter.
counterName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.mapping.MappingCounters: Get the name of the counter.
Counters - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define the counters names used in this package.
Counters() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
CounterSequenceFile - Interface in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This interface extends SequenceFile to add a getCount() method that allow to get the count of the read entries.
CountSplicedReadsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc: This step computes how many spliced alignments there are in a SAM file.
CountSplicedReadsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule
cpuInfo() - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with CPU informations.
create() - Method in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Create the ports.
create() - Method in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Create the ports.
create() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Create an OutputStream for the DataFile.
create() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
createBZip2InputStream(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs: Create a bzip2 input stream.
createBZip2InputStream(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.HadoopCompressionCodecs: Create a bzip2 input stream.
createBZip2OutputStream(OutputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.ApacheCommonCompressionCodecs: Create a bzip2 output stream.
createBZip2OutputStream(OutputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.io.HadoopCompressionCodecs: Create a bzip2 output stream.
createCommand(File, boolean, String, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor: Create R command.
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
createCommandLine(String) - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter: Create the command line for the the argument of the interpreter.
createCommandLine(String) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
createConfiguration() - Static method in class fr.ens.biologie.genomique.eoulsan.CommonHadoop: Create a new Configuration object from Eoulsan runtime settings.
createConfiguration(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.CommonHadoop: Create a new Configuration object from settings.
CREATED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
CreateDesignAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action to create design file.
CreateDesignAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
createEmptyDesign() - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignFactory: Create a design without targets.
createEoulsanDataDirectoryIfRequired() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Create an "eoulsan-data" directory if mapper indexes or genome description storage has not been defined.
createFileInTempDir(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a file in the temporary directory.
createGenomeDescription(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator: Create genome description object from the storage if already exists or compute it from the genome.
createGenomeDescriptionFromAnnotation(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator: Create genome description object from the storage if already exists or compute it from the genome.
CreateHadoopJarAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action to create hadoop jar file.
CreateHadoopJarAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
createIndex(DataFile, GenomeDescription, DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeMapperIndexer: Create an archived genome index.
createInputStream(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Create an input stream from a path.
createLogFileAndFlushLog(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Create a new log file and flush log.
createLogFiles(URI, URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Create the log file for Eoulsan and additional log file for dependencies that use their own logging system.
createOtherLog(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Create the additional log file for dependencies that use their own logging system.
createOutputStream(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Create an output stream from a path.
createRecordReader(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqInputFormat
createRecordReader(InputSplit, TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMInputFormat
createSAMSequenceDictionaryFromSAMHeader(List<String>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMHeaderHadoopUtils: Create a SAMSequenceDictionary from the SAM header in a list of String.
createShutdownHookThread() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Create a shutdown hook thread.
createSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
createSimpleProcess() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor: Create the process that will execute the R Script.
createStepResult(TaskContextImpl, Throwable) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Create a step result for an exception.
createStepResult(TaskContextImpl, Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Create a step result for an exception.
createTaskResult() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Create a TaskResult object for a successful result.
createTaskResult() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
createTaskResult(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Create a TaskResult object.
createTaskResult(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
createTaskResult(Throwable) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Create a TaskResult object.
createTaskResult(Throwable) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
createTaskResult(Throwable, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Create a TaskResult object.
createTaskResult(Throwable, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
createTempDir() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a new temporary directory.
createTempDir(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a new temporary directory.
createTempFile(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a new temporary file.
createTempPath(Path, String, String, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Create a new temporary path.
CUTADAPT_ADAPTER_FASTA - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Cutadapt adapters format.

D

Data - Interface in fr.ens.biologie.genomique.eoulsan.data: This interface define data used by ports.
DATA_FORMAT_PATH_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.Settings
dataEquals(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if two files are related to the same data.
dataEquals(File, File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if two files are related to the same data.
dataEquals(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Test if two filenames are related to the same data.
DataFile - Class in fr.ens.biologie.genomique.eoulsan.data: This class define a DataFile.
DataFile(DataFile, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(File, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(URI) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(Path) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
DataFile(Path, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFile: Public constructor.
dataFileCount(StepOutputPort, Sample, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the count of files that exists for a step, a format and sample (case of multi-files data).
DataFileDataPath - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a bridge between Kenetre DataPath objects and Eoulsan DataFile objects.
DataFileDataPath(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath: Constructor.
DataFileDataPath(DataPath, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath: Constructor.
DataFileDataPath(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath: Constructor.
DataFileDistCp - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This class allow to copy and transform data in a distributed manner.
DataFileDistCp(Configuration, Path) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp: Public constructor.
DataFileDistCp.DistCpMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This inner class define the mapper class for DataSourceDistCp map-reduce job.
DataFileGenomeDescStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a storage for genome description files using DataFile API.
DataFileGenomeDescStorage(DataPath, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage: Protected constructor.
DataFileGenomeIndexStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a storage for genome indexes using DataFile API.
DataFileGenomeIndexStorage(DataPath, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage: Constructor.
DataFileGenomeMapperIndexer - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a genome mapper indexer.
DataFileGenomeMapperIndexer(MapperInstance, String, Map<String, String>, int, GenomeIndexStorage, File, GenericLogger) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeMapperIndexer: Public constructor.
DataFileMetadata - Interface in fr.ens.biologie.genomique.eoulsan.data: This class define source metadata
DataFiles - Class in fr.ens.biologie.genomique.eoulsan.data: This class contains utility methods on DataFile objects.
DataFiles() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFiles
DataFileStorage - Class in fr.ens.biologie.genomique.eoulsan.data.storages: This class define a storage using DataFile API.
DataFileStorage(String, List<String>) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage: Constructor.
DataFormat - Interface in fr.ens.biologie.genomique.eoulsan.data: This interface define a DataFormat.
DataFormatConverter - Class in fr.ens.biologie.genomique.eoulsan.data: This class allow to copy and transform data while copying.
DataFormatConverter(DataFile, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter: Constructor
DataFormatConverter(DataFile, DataFile, DataFormat, OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter: Constructor
DataFormatConverter(DataFile, DataFile, OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormatConverter: Constructor
DataFormatRegistry - Class in fr.ens.biologie.genomique.eoulsan.data: this class register DataFormat to allow get the DataFormat of a file from its filename.
DataFormats - Class in fr.ens.biologie.genomique.eoulsan.data: This class contains the definition of some DataFormats.
DataFormats() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.DataFormats
DATAFORMATS_TO_DOWNLOAD_SETTING - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule: Key in the settings to use to save the list of DataFormat of the files to download.
DataList - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a data list.
DataMetadata - Interface in fr.ens.biologie.genomique.eoulsan.data: This interface define metadata of data objects.
DataMetadataStorage - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a storage for data metadata of all files generated by the workflow.
DataProtocol - Interface in fr.ens.biologie.genomique.eoulsan.data.protocols: This interface define a protocol.
DataProtocolService - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a service to retrieve a DataProtocol.
DataToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: The Class ToolOutputsData.
DataToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement: Instantiates a new tool outputs data.
DataUtils - Class in fr.ens.biologie.genomique.eoulsan.core: This class define an utility on data object.
DATE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
deadEvent(DeadEvent) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus
DEBUG - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Set the debug mode.
decompressInputStreamIsNeeded(InputStream, String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Decompress an inputStream if needed.
DeepToolsModule - Class in fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling: This class uses tools from the DeepTools suite.
DeepToolsModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
DEFAULT_CHARSET - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Default charset.
DEFAULT_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Default file encoding.
DEFAULT_LOCALE - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Default locale of the application.
DEFAULT_R_LANG - Static variable in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
DEFAULT_SINGLE_INPUT_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.InputPortsBuilder: Default single input port name.
DEFAULT_SINGLE_OUTPUT_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.OutputPortsBuilder: Default single output port name.
DefaultDesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class allow to read a design file whatever the underlying design format.
DefaultDesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader: Public constructor.
DefaultDesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader: Public constructor.
DefaultDesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader: Public constructor
DefaultDesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DefaultDesignReader: Public constructor
DefaultExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This class define the default executor interpreter.
DefaultExecutorInterpreter() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
DefineDataFormatToDownload - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This Step allow to define the list of the formats of the files to download at the end of a Hadoop execution.
DefineDataFormatToDownload() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
defineSampleSubDirName(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Get the sample sub directory.
delete() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Delete the DataFile.
delete(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Delete the DataFile.
delete(DataFile, boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Delete a file.
delete(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
delete(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
deleteOnExit(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
deleteOnExit(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Delete a file on the exit of the workflow.
DeprecatedDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a deprecated protocol.
DeprecatedDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol: Constructor.
DeprecatedDataProtocol(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol: Constructor.
deprecatedParameter(StepConfigurationContext, Parameter) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters.
deprecatedParameter(StepConfigurationContext, Parameter, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters.
deprecatedParameter(String, Parameter, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Show a message for deprecated parameters.
description() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
DESCRIPTION_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
DESeq2 - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class contains methods to run the differential analysis module DESeq2.
DESeq2(RExecutor, String, Design, Experiment, Map<String, File>, boolean, boolean, boolean, boolean, DESeq2.SizeFactorsType, DESeq2.FitType, DESeq2.StatisticTest, boolean) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2: Public constructor.
DESeq2.FitType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Enum for the fitType option in DESeq2 related to the dispersion estimation.
DESeq2.SizeFactorsType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Enum for the sizeFactorsType option in DESeq2 related to the estimation of the size factor.
DESeq2.StatisticTest - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Enum for the statisticTest option in DESeq2 related to the statistic test to be used during the differential expression analysis
DESeq2DesignChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a Checker on the design for DESeq2 analyzes.
DESeq2DesignChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
DESeq2Module - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: Class to run the differential analysis with DEseq2
DESeq2Module() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
deserialize(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize the TaskContext object.
deserialize(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Deserialize the TaskResult object.
deserialize(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize the TaskContext object.
deserialize(File) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Deserialize the TaskResult object.
deserialize(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize the TaskContext object.
deserialize(InputStream) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl: Deserialize the TaskResult object.
deserializeOutputData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize output data.
deserializeOutputData(File) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize output data.
deserializeOutputData(InputStream) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Deserialize output data.
design - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Design - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the design.
DESIGN_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata
DESIGN_FILE_PATH_CONSTANT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowParser: Design file path constant name.
DESIGN_FILE_VERSION - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Design file version.
DESIGN_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
DesignBuilder - Class in fr.ens.biologie.genomique.eoulsan.design: This class allow to easily build Design object from files paths.
DesignBuilder() - Constructor for class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Public constructor.
DesignBuilder(String[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Public constructor.
DesignFactory - Class in fr.ens.biologie.genomique.eoulsan.design: This class is a factory for experimental design.
DesignFormatFinderInputStream - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class allow to automatically detect the format of a design file.
DesignFormatFinderInputStream(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream: Public constructor.
DesignMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the design metadata.
DesignMetadataImpl - Class in fr.ens.biologie.genomique.eoulsan.design: This class defines the default implementation of the design metadata.
DesignModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a design module.
DesignModule(Design, CheckerModule) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.DesignModule: Constructor.
DesignReader - Interface in fr.ens.biologie.genomique.eoulsan.design.io: This interface define a DesignReader.
DesignUtils - Class in fr.ens.biologie.genomique.eoulsan.design: Utils methods for Design.
DesignWriter - Interface in fr.ens.biologie.genomique.eoulsan.design.io: This interface define a writer for designs.
DiffAna - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class create and launch a R script to compute differential analysis.
DiffAna(RExecutor, Design, DiffAna.DispersionMethod, DiffAna.DispersionSharingMode, DiffAna.DispersionFitType) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna: Public constructor.
DIFFANA_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Diffana results data format.
DiffAna.DispersionFitType - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Dispersion estimation fitType enum for DESeq differential analysis
DiffAna.DispersionMethod - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Dispersion estimation method enum for DESeq differential analysis
DiffAna.DispersionSharingMode - Enum in fr.ens.biologie.genomique.eoulsan.modules.diffana: Dispersion estimation sharingMode enum for DESeq differential analysis
DiffAnaModule - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class define the module of differential analysis in local mode.
DiffAnaModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
DiffanaResultsAnnotationModule - Class in fr.ens.biologie.genomique.eoulsan.modules.diffana: This class define a module that create annotated expression files in TSV, ODS or XLSX format.
DiffanaResultsAnnotationModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
disConnect() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Destroy the connection to the Rserve server.
DISCUSSION_GROUP - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Project discussion group.
diskFreeInfo(File) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Get information about the partition of a file.
DistCp - Class in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop: A Map-reduce program to recursively copy directories between different file-systems.
DistCp(Configuration) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
DistCp.DuplicationException - Exception in fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop: An exception class for duplicated source files.
DistCpMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DataFileDistCp.DistCpMapper
DistributedLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker: Distributed locking via ZooKeeper.
DistributedLock(ZooKeeper, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock
DistributedLock(ZooKeeper, String, Iterable<ACL>) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLock: Creates a distributed lock using the given zkClient to coordinate locking.
DistributedLocker - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class implements a locker using Zookeeper based on Twiter's DistributedLock class.
DistributedLocker(String, int, String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.DistributedLocker: Public constructor.
DOCKER - fr.ens.biologie.genomique.eoulsan.util.r.RExecutorFactory.Mode
DOCKER_IMAGE_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
DockerExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This class define a Docker executor interpreter.
DockerExecutorInterpreter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter: Constructor.
dockerInfo(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with Docker configuration informations.
DockerRequirement - Class in fr.ens.biologie.genomique.eoulsan.requirements: This class define a Docker requirement.
DockerRequirement() - Constructor for class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
DockerRExecutor - Class in fr.ens.biologie.genomique.eoulsan.util.r: This class define a Docker RExecutor.
DockerRExecutor(File, File, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor: Constructor.
DONE - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
DUMMY_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Dummy format.
DummyGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class implements a dummy generator module that create an empty file.
DummyGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
DummyTaskScheduler - Class in fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This class define a Dummy cluster scheduler.
DummyTaskScheduler() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler: Constructor.

E

elapsed(TimeUnit) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.SerializableStopwatch
ELIMINATED_READS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
EmergencyStopTask - Interface in fr.ens.biologie.genomique.eoulsan.core.workflow: This interface define a task that will executed if the execution of the workflow fail.
EmergencyStopTasks - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class define a class where the emergency tasks are stored
EMPTY_ALIGNMENTS_COUNTER - fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter
EmptyFileQC - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: Empty file FastQC module.
EmptyFileQC(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC: Constructor.
EmptyToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define an empty tool element.
EmptyToolElement() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement: Public constructor.
EmptyToolElement(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement: Public constructor.
EmptyToolElement(String, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement: Public constructor.
encodeAllowedCompressionsParameterValue(EnumSet<CompressionType>) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule: Method to encode an EnumSet of the allowed compressions parameter in a string.
endWork(Ticket) - Method in interface fr.ens.biologie.genomique.eoulsan.util.locker.TicketScheduler: Inform the scheduler that the ticket job has been finished.
endWork(Ticket) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.TicketSchedulerServer
ENTRIES_READ - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
ENTRIES_WRITTEN - Static variable in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.Counters
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
entrySet() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get an entry set of the metadata.
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
entrySet() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
EOULSAN_CLASSPATH_JVM_ARG - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
EOULSAN_MEMORY - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
EOULSAN_PATH - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
EOULSAN_SCRIPT - Static variable in class fr.ens.biologie.genomique.eoulsan.Main
EOULSAN_TOOLS_WEBSITE_URL - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: Eoulsan tools website URL.
Eoulsan1DesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class define a design reader for limma design files.
Eoulsan1DesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader: Public constructor.
Eoulsan1DesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader: Public constructor.
Eoulsan1DesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader: Public constructor.
Eoulsan1DesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignReader: Public constructor.
Eoulsan1DesignWriter - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class implements a writer for limma design files.
Eoulsan1DesignWriter(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter: Public constructor.
Eoulsan1DesignWriter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter: Public constructor.
Eoulsan1DesignWriter(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter: Public constructor.
Eoulsan1DesignWriter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan1DesignWriter: Public constructor.
Eoulsan2DesignReader - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class define a design reader for Eoulsan 2 design file.
Eoulsan2DesignReader(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader: Public constructor.
Eoulsan2DesignReader(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader: Public constructor.
Eoulsan2DesignReader(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader: Public constructor.
Eoulsan2DesignReader(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignReader: Public constructor.
Eoulsan2DesignWriter - Class in fr.ens.biologie.genomique.eoulsan.design.io: This class implements a writer for Eoulsan 2 design files.
Eoulsan2DesignWriter(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter: Public constructor.
Eoulsan2DesignWriter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter: Public constructor.
Eoulsan2DesignWriter(OutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter: Public constructor.
Eoulsan2DesignWriter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.design.io.Eoulsan2DesignWriter: Public constructor.
EoulsanAnnotationUtils - Class in fr.ens.biologie.genomique.eoulsan.annotations: This class contains annotation utilities.
EoulsanDockerManager - Class in fr.ens.biologie.genomique.eoulsan.util: This class define a Docker manager configurated with Eoulsan settings.
EoulsanError - Error in fr.ens.biologie.genomique.eoulsan: A nestable Eoulsan error.
EoulsanError() - Constructor for error fr.ens.biologie.genomique.eoulsan.EoulsanError: Create a new EoulsanError.
EoulsanError(String) - Constructor for error fr.ens.biologie.genomique.eoulsan.EoulsanError: Create a new EoulsanError with a message.
EoulsanException - Exception in fr.ens.biologie.genomique.eoulsan: A nestable Eoulsan exception.
EoulsanException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException: Create a new EoulsanException.
EoulsanException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException: Create a new EoulsanException with a message.
EoulsanException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException: Create a new EoulsanException with a message and a cause.
EoulsanException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanException: Create a new EoulsanException with a cause.
EoulsanITRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan: This class define a runtime exception for integration tests.
EoulsanITRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException: Create a new EoulsanITRuntimeException.
EoulsanITRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException: Create a new EoulsanITRuntimeException with a message.
EoulsanITRuntimeException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException: Create a new EoulsanITRuntimeException with a message and a cause.
EoulsanITRuntimeException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanITRuntimeException: Create a new EoulsanITRuntimeException with a cause.
EoulsanLogger - Class in fr.ens.biologie.genomique.eoulsan: This class allow to change the logger name for all Eoulsan classes.
EoulsanLogger() - Constructor for class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
EoulsanRuntime - Class in fr.ens.biologie.genomique.eoulsan: This class store the only Eoulsan runtime instance.
EoulsanRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan: A nestable Eoulsan exception.
EoulsanRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException: Create a new EoulsanRuntimeException.
EoulsanRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException: Create a new EoulsanRuntimeException with a message.
EoulsanRuntimeException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException: Create a new EoulsanException with a message and a cause.
EoulsanRuntimeException(Throwable) - Constructor for exception fr.ens.biologie.genomique.eoulsan.EoulsanRuntimeException: Create a new EoulsanException with a cause.
EoulsanTranslatorUtils - Class in fr.ens.biologie.genomique.eoulsan.util: This class define Kenetre translator utility glue methods for Eoulsan.
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterJobEmergencyStopTask
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
equals(Object) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopJobEmergencyStopTask
equals(Object) - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
ERROR_CODE - Static variable in exception fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp.DuplicationException: Error code for this exception
errorExit(Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print error message to the user and exits the application.
errorExit(Throwable, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print error message to the user and exits the application.
errorHalt(Throwable, String) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print error message to the user and halts the application.
errorHalt(Throwable, String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Print error message to the user and halts the application.
escapeUnderScore(String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Escape underscore for LaTeX title.
exceptionMessage - Variable in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessThreadErrOutput
exec(String, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command with the OS.
ExecAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define the Local exec Action.
ExecAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
ExecFileLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class define a lock file.
ExecFileLock(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecFileLock: Public constructor.
ExecJarHadoopAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action that allow to execute a jar on an Hadoop cluster.
ExecJarHadoopAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
ExecLock - Class in fr.ens.biologie.genomique.eoulsan.util.locker: This class define a lock to prevent execution of a process simultaneously on multiples JVM.
ExecLock(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock: Public constructor.
ExecLock(String, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock: Public constructor.
execThreadOutput(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command and write the content of the standard output and error to System.out and System.err.
execThreadOutput(String[]) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command and write the content of the standard output and error to System.out and System.err.
execToString(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command with the OS and return the output in a string.
execToString(String, boolean, boolean) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command with the OS and return the output in a string.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Execute the workflow.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor: run Eoulsan.
execute() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.CheetahInterpreter: Execute script by Python interpreter and replace variable name by value.
execute(TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Convert command tag from tool file in string, variable are replace by value.
execute(TaskContext, TaskStatus) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Execute a task step.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Merge input replicates.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule: Run bedtools multiinter.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule: Run deeptools.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module: Run macs2.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Install all the files necessary in the tmp folder, then run idr.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Install all the files necessary in the tmp folder, then run idr.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule: Run trackhub generator.
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.local.ExpressionLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAM2BAMHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterHadoopModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.BAM2SAMLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsFilterLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2BAMLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAM2FASTQLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.SAMFilterLocalModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.Splice2BEDModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
execute(TaskContext, TaskStatus) - Method in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
execute(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils: Execute a task context serialization file.
execute(DataFile, DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskSerializationUtils: Execute a task context serialization file.
execute(List<Module>, List<Module>) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor: run Eoulsan.
execute(List<String>, File, File, File, File, File...) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.AbstractExecutorInterpreter
execute(List<String>, File, File, File, File, File...) - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter: Execute a command line.
executeRCode(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Execute a R code.
executeRnwCode(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Execute a R Sweave code.
executeRnwCode(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Execute a R Sweave code.
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Execute a R script.
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
executeRScript(File, boolean, String, File, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
executeRScript(String, boolean, String, boolean, String, DataFile, String...) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
executeRScript(String, boolean, String, boolean, String, DataFile, String...) - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Execute a R script.
executeTask(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Default executing context method.
EXECUTION_MODE_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.RModuleCommonConfiguration
ExecutionMode - Enum in fr.ens.biologie.genomique.eoulsan.annotations: This class define an enum for the execution mode of Eoulsan.
executor - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
Executor - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class is the executor for running all the steps of an analysis.
Executor(ExecutorArguments) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.Executor: Constructor.
ExecutorArguments - Class in fr.ens.biologie.genomique.eoulsan.core.workflow: This class contains arguments for the Executor.
ExecutorArguments() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Public constructor.
ExecutorArguments(long) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Public constructor.
ExecutorArguments(File, File) - Constructor for class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Public constructor.
ExecutorInterpreter - Interface in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This interface define a executor interpreter for Galaxy tools.
execWriteOutput(String, File) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Execute a command with the OS and save the output in file.
exists() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Check if this DataFile exists.
exists() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
exists(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Check if this DataFile exists.
exists(DataFile, boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Test a source exists.
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
exists(DataFile, boolean) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
exists(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Test if a path exists
exit(int) - Static method in class fr.ens.biologie.genomique.eoulsan.Common: Exit the application.
Experiment - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines an experiment.
ExperimentImpl - Class in fr.ens.biologie.genomique.eoulsan.design: This class defines the default implementation of an experiment.
ExperimentMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the experiment metadata.
ExperimentSample - Interface in fr.ens.biologie.genomique.eoulsan.design: This interface defines the experiment sample.
ExperimentSampleImpl - Class in fr.ens.biologie.genomique.eoulsan.design: This class defines the default implementation of the experiment sample.
ExperimentSampleMetadata - Interface in fr.ens.biologie.genomique.eoulsan.design: This inteface defines the experiment sample metadata.
ExperimentSampleMetadataImpl - Class in fr.ens.biologie.genomique.eoulsan.design: This class defines the default implementation of the experiment sample metadata.
EXPRESSION_MATRIX_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Expression matrix.
EXPRESSION_RESULTS_TSV - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Expression results data format.
ExpressionCounterCounter - Enum in fr.ens.biologie.genomique.eoulsan.modules.expression: This enum define counters for the expression step.
ExpressionCounterUtils - Class in fr.ens.biologie.genomique.eoulsan.modules.expression: This class define some glue methods between Eoulsan and Kenetre.
expressionFilesPrefix - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
expressionFilesSuffix - Variable in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization
ExpressionHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: This class is the main class for the expression program of the reads in hadoop mode.
ExpressionHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
ExpressionInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a preprocessor for expression reports.
ExpressionInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
ExpressionLocalModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.local: This class is the module to compute expression in local mode
ExpressionLocalModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.local.ExpressionLocalModule
ExpressionMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: Mapper for the expression estimation.
ExpressionMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionMapper
ExpressionMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a merger class for expression files.
ExpressionMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
ExpressionOutputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a expression output format.
ExpressionOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionOutputFormat
ExpressionRecordWriter - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a RecordWriter for expression files.
ExpressionRecordWriter(TaskAttemptContext, DataOutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionRecordWriter: Public constructor.
ExpressionReducer - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: Reducer for the expression estimation.
ExpressionReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionReducer
ExpressionResultsAnnotationModule - Class in fr.ens.biologie.genomique.eoulsan.modules.expression: This class define a module that create annotated expression files in TSV, ODS or XLSX format.
ExpressionResultsAnnotationModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
ExpressionSAMOutputMapper - Class in fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: Mapper for the expression estimation with a SAM output.
ExpressionSAMOutputMapper() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionSAMOutputMapper
ExpressionSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a splitter class for expression files.
ExpressionSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
ExpressionToMatrixModule - Class in fr.ens.biologie.genomique.eoulsan.modules.singlecell: This class define a class that allow to merge expression file into a matrix file.
ExpressionToMatrixModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
EXTERNAL_APP - fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime.EoulsanExecMode
extractCheetahScript(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract command tag in string.
extractChildElementsByTagName(Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract child elements by tag name.
extractConditionalParamElement(ToolInfo, Element) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract conditional param element.
extractConditionalParamElement(ToolInfo, Element, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract conditional param element.
extractDescription(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract description tag in string.
extractDockerImage(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract docker image attribute in string.
extractElementsByTagName(ToolInfo, Document, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract elements by tag name.
extractElementsByTagName(ToolInfo, Document, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract elements by tag name.
extractElementsByTagName(Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract elements by tag name.
extractElementsByTagName(Element, String, int) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract elements by tag name.
extractInputs(ToolInfo, Document, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract all input parameters define in document.
extractInterpreters(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract interpreter attribute in string.
extractOutputs(ToolInfo, Document, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract all output parameters define in document.
extractParamElement(ToolInfo, Element, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract parameter elements.
extractParamElement(ToolInfo, Element, String, Map<String, Parameter>) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract parameter elements.
extractToolID(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract tool id tag in string.
extractToolName(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract tool name tag in string.
extractToolVersion(Document) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract tool version attribute in string.
extractValueFromElement(Document, String, int, String) - Static method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils: Extract text from DOM from tag name, at the index place.

F

FAILED - fr.ens.biologie.genomique.eoulsan.core.Step.StepState
FailModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This module is a module that always fails.
FailModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FailModule
FakeModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This module is a fake module.
FakeModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
FASTA_FILE_WIDTH - Static variable in class fr.ens.biologie.genomique.eoulsan.Globals: FASTA file width.
FASTQ_FORMAT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata
FASTQ_FORMAT_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata
FASTQC_CASAVA_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Format fastq type casava/Illumina
FASTQC_EXPGROUP_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Use exponential base groups in graph
FASTQC_KMER_SIZE_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Collector FastQC kmer size
FASTQC_NOFILTER_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Option for filter fastq file if casava=true for all modules
FASTQC_NOGROUP_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule: Collector FastQC nogroup
FASTQC_REPORT_HTML - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: FastQC HTML report format.
FASTQC_REPORT_ZIP - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: FastQC ZIP report format.
FastQCInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a preprocessor for FastQC reports.
FastQCInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
FastQCModule - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This class define a module that compute QC report using FastQC.
FastQCModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
FastQCRuntimePatcher - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This class to patch FastQC to be compatible with Hadoop.
FastQCRuntimePatcher() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCRuntimePatcher
FastqInputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define an InputFormat for FASTQ files for the Hadoop MapReduce framework.
FastqInputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqInputFormat
FastqLineRecordReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: Treats keys as offset in file and value as line.
FastqLineRecordReader() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
FastqLineRecordReader(byte[]) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
FastqMerger - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a merger class for FASTQ files.
FastqMerger() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
FastqOutputFormat - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a FASTQ output format.
FastqOutputFormat() - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqOutputFormat
FastqPairedEndReducer() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.PairedEndFastqToTfq.FastqPairedEndReducer
FastqRecordReader - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a RecordReader for FASTQ files for the Hadoop MapReduce framework.
FastqRecordReader(TaskAttemptContext) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader: Public constructor.
FastqRecordWriter - Class in fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This class define a RecordWriter for FASTQ files.
FastqRecordWriter(TaskAttemptContext, DataOutputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordWriter: Public constructor.
FastqSequenceFile - Class in fr.ens.biologie.genomique.eoulsan.modules.fastqc: This class define a SequenceFile for FASTQ files.
FastqSequenceFile(DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile: Public constructor.
FastqSplitter - Class in fr.ens.biologie.genomique.eoulsan.splitermergers: This class define a splitter class for FASTQ files.
FastqSplitter() - Constructor for class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
FEATURECOUNTS_SUMMARY_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: FeatureCounts summary format.
FeatureCountsInputPreprocessor - Class in fr.ens.biologie.genomique.eoulsan.modules.multiqc: This class define a preprocessor for FeatureCounts reports.
FeatureCountsInputPreprocessor() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
FEATURES_FILE_FORMAT_PARAMETER_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
file(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create a DataFile object for a file of the workflow.
FileCharsets - Class in fr.ens.biologie.genomique.eoulsan.io: This class define default charsets.
FileConcatInputStream - Class in fr.ens.biologie.genomique.eoulsan.io: This class define an InputStream that concatenate files in an InputStream.
FileConcatInputStream(List<File>) - Constructor for class fr.ens.biologie.genomique.eoulsan.io.FileConcatInputStream: Constructor.
FileDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class implements a File Protocol.
FileDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
fileMiddle() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the middle string of the filename.
fileMiddle(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the middle of a filename.
fileMiddle(StepOutputPort, String, int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the middle of a filename.
fileMiddle(String, int, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the middle of a filename.
filename() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the filename.
filename(StepOutputPort, DataElement, int) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the name of a data file of the workflow.
filename(String, String, DataFormat, String, int, int, CompressionType) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the filename from several parameters.
FileNaming - Class in fr.ens.biologie.genomique.eoulsan.core: This class contains methods to create workflow data file names.
FileNaming() - Constructor for class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Private constructor.
FileNamingParsingRuntimeException - Exception in fr.ens.biologie.genomique.eoulsan.core: This class define a runtime exception for filename parsing errors.
FileNamingParsingRuntimeException() - Constructor for exception fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException: Create a new FileNamingParsingRuntimeException.
FileNamingParsingRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.eoulsan.core.FileNamingParsingRuntimeException: Create a new FileNamingParsingRuntimeException with a message.
filePrefix() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the file prefix.
filePrefix(StepOutputPort) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the prefix of a filename.
filePrefix(String, String, DataFormat) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the prefix of a filename.
filePrefix(String, String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the prefix of a filename.
FileResourceLoader<S> - Class in fr.ens.biologie.genomique.eoulsan.util: This class allow to define a resource loader for files.
FileResourceLoader(Class<S>, DataFile) - Constructor for class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Public constructor.
fileSuffix() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Return the file suffix.
fileSuffix(StepOutputPort) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowFileNaming: Create the suffix of a filename.
fileSuffix(DataFormat, CompressionType) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the suffix of a file.
fileSuffix(String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Create the suffix of a file.
fillBuffer(InputStream, byte[], boolean) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.CompressedSplitFastqLineReader
FilterAndMapReadsHadoopModule - Class in fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This class define a Step that filter and map read in Hadoop mode.
FilterAndMapReadsHadoopModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
FinalExpressionFeaturesCreator - Class in fr.ens.biologie.genomique.eoulsan.modules.expression: This class generates the final expression file after counting the alignments for each feature with HTSeq-count.
FinalExpressionFeaturesCreator(ExpressionCounter) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.expression.FinalExpressionFeaturesCreator: Public constructor.
FIRST_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
FirstModule - Class in fr.ens.biologie.genomique.eoulsan.modules: This class define a first module that do nothing.
FirstModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
FIT_ONLY - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
FloatParameterToolElement - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This class define a float tool element parameter.
FloatParameterToolElement(ToolInfo, Element) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement: Instantiates a new float tool parameter.
FloatParameterToolElement(ToolInfo, Element, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.FloatParameterToolElement: Instantiates a new float tool parameter.
flush() - Method in class fr.ens.biologie.genomique.eoulsan.BufferedHandler
flush() - Method in class fr.ens.biologie.genomique.eoulsan.io.ProgressCounterOutputStream
flushLog() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Flush log.
FORMAT_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
FORMATS_PARAMETER - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
FormatsAction - Class in fr.ens.biologie.genomique.eoulsan.actions: This class define an action that show the list of available formats.
FormatsAction() - Constructor for class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
fr.ens.biologie.genomique.eoulsan - package fr.ens.biologie.genomique.eoulsan: Root package of Eoulsan.
fr.ens.biologie.genomique.eoulsan.actions - package fr.ens.biologie.genomique.eoulsan.actions: This package contains all the commands (actions) available through the Eoulsan command line.
fr.ens.biologie.genomique.eoulsan.annotations - package fr.ens.biologie.genomique.eoulsan.annotations: This package define the annotations on Eoulsan classes plug-ins.
fr.ens.biologie.genomique.eoulsan.bio.io.hadoop - package fr.ens.biologie.genomique.eoulsan.bio.io.hadoop: This package contains I/O classes for reading objects of the fr.ens.biologie.genomique.eoulsan.bio.alignmentsfilters package from Hadoop.
fr.ens.biologie.genomique.eoulsan.checkers - package fr.ens.biologie.genomique.eoulsan.checkers: This package contains and define checkers of DataFormat.
fr.ens.biologie.genomique.eoulsan.core - package fr.ens.biologie.genomique.eoulsan.core: This package contains Eoulsan workflow core class.
fr.ens.biologie.genomique.eoulsan.core.schedulers - package fr.ens.biologie.genomique.eoulsan.core.schedulers: This package contains classes for schedulers.
fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters - package fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters: This package contains classes for cluster schedulers.
fr.ens.biologie.genomique.eoulsan.core.workflow - package fr.ens.biologie.genomique.eoulsan.core.workflow: This package contains Eoulsan workflow dedicated classes.
fr.ens.biologie.genomique.eoulsan.data - package fr.ens.biologie.genomique.eoulsan.data: This package contains classes for data files, data types and data formats.
fr.ens.biologie.genomique.eoulsan.data.protocols - package fr.ens.biologie.genomique.eoulsan.data.protocols: This package contains class for protocols used by the DataFile classes.
fr.ens.biologie.genomique.eoulsan.data.storages - package fr.ens.biologie.genomique.eoulsan.data.storages: This package contains and define data storages.
fr.ens.biologie.genomique.eoulsan.design - package fr.ens.biologie.genomique.eoulsan.design: This package contains classes to handle experimental designs.
fr.ens.biologie.genomique.eoulsan.design.io - package fr.ens.biologie.genomique.eoulsan.design.io: This package contains I/O classes to read and write design files.
fr.ens.biologie.genomique.eoulsan.galaxytools - package fr.ens.biologie.genomique.eoulsan.galaxytools: This package contain classes related to read tool xml file from galaxy.
fr.ens.biologie.genomique.eoulsan.galaxytools.elements - package fr.ens.biologie.genomique.eoulsan.galaxytools.elements: This package contain classes related to parameter extractions from XML Galaxy tool xml files.
fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters - package fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This package contain classes related to the Galaxy tool executor interpreters.
fr.ens.biologie.genomique.eoulsan.io - package fr.ens.biologie.genomique.eoulsan.io: This package contains general I/O classes for Eoulsan (not dedicated to fr.ens.biologie.genomique.eoulsan.bio package).
fr.ens.biologie.genomique.eoulsan.modules - package fr.ens.biologie.genomique.eoulsan.modules: This package define the steps for the Eoulsan workflow.
fr.ens.biologie.genomique.eoulsan.modules.chipseq - package fr.ens.biologie.genomique.eoulsan.modules.chipseq: This packages contains the ChIP-Seq modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling - package fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling: This packages contains the peak-calling modules.
fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc - package fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc: This packages contains all the quality check modules for ChIP-Seq.
fr.ens.biologie.genomique.eoulsan.modules.diffana - package fr.ens.biologie.genomique.eoulsan.modules.diffana: This package contain all the classes related to the differential analysis step.
fr.ens.biologie.genomique.eoulsan.modules.expression - package fr.ens.biologie.genomique.eoulsan.modules.expression: This package contain all the classes related to the expression step.
fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop - package fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop: This package contain all the classes related to the expression step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.expression.local - package fr.ens.biologie.genomique.eoulsan.modules.expression.local: This package contain all the classes related to the expression step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.fastqc - package fr.ens.biologie.genomique.eoulsan.modules.fastqc: This package contain all the classes related to FastQC.
fr.ens.biologie.genomique.eoulsan.modules.generators - package fr.ens.biologie.genomique.eoulsan.modules.generators: This package contain generator steps.
fr.ens.biologie.genomique.eoulsan.modules.mapping - package fr.ens.biologie.genomique.eoulsan.modules.mapping: This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop - package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop: This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli - package fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli
fr.ens.biologie.genomique.eoulsan.modules.mapping.local - package fr.ens.biologie.genomique.eoulsan.modules.mapping.local: This package contain all the classes related to the mapping (reads filtering, mapping and alignments filtering) step in local mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt - package fr.ens.biologie.genomique.eoulsan.modules.mgmt: This package contain classes related data management (e.g.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop - package fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop: This package contain classes related data management in Hadoop mode.
fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload - package fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload: This package contain classes related to upload data to HDFS and Cloud.
fr.ens.biologie.genomique.eoulsan.modules.multiqc - package fr.ens.biologie.genomique.eoulsan.modules.multiqc
fr.ens.biologie.genomique.eoulsan.modules.singlecell - package fr.ens.biologie.genomique.eoulsan.modules.singlecell
fr.ens.biologie.genomique.eoulsan.requirements - package fr.ens.biologie.genomique.eoulsan.requirements: This package contains requirement classes for Eoulsan.
fr.ens.biologie.genomique.eoulsan.splitermergers - package fr.ens.biologie.genomique.eoulsan.splitermergers: This package contains splitter and merger used when running Eoulsan on a standard cluster to get more parallelization efficiency.
fr.ens.biologie.genomique.eoulsan.ui - package fr.ens.biologie.genomique.eoulsan.ui: This package contains Eoulsan user interface classes.
fr.ens.biologie.genomique.eoulsan.util - package fr.ens.biologie.genomique.eoulsan.util: This package contain utility classes.
fr.ens.biologie.genomique.eoulsan.util.hadoop - package fr.ens.biologie.genomique.eoulsan.util.hadoop: This package contains utility classes for hadoopS.
fr.ens.biologie.genomique.eoulsan.util.locker - package fr.ens.biologie.genomique.eoulsan.util.locker: This package contain an advanced multi JVM lock system.
fr.ens.biologie.genomique.eoulsan.util.r - package fr.ens.biologie.genomique.eoulsan.util.r: This package contain utility classes for R usage.
FTPPathDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the FTP protocol in Hadoop mode.
FTPPathDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol
FTPURLDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define the ftp protocol in local mode.
FTPURLDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol
fullyDelete(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Fully delete a file of the content of a directory

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GALAXY_TOOL_PATH_KEY - Static variable in class fr.ens.biologie.genomique.eoulsan.Settings
GalaxyToolInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: This class create an interpreter to tool xml file from Galaxy.
GalaxyToolInterpreter(File) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Public constructor.
GalaxyToolInterpreter(InputStream, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Public constructor.
GalaxyToolModule - Class in fr.ens.biologie.genomique.eoulsan.modules: The Class GalaxyToolStep.
GalaxyToolModule(InputStream) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule: Constructor.
GalaxyToolModule(InputStream, String) - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule: Constructor.
GalaxyToolXMLParserUtils - Class in fr.ens.biologie.genomique.eoulsan.galaxytools: This class define static utils methods to extract data in Galaxy tool XML file.
GalaxyToolXMLParserUtils() - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolXMLParserUtils
GAPPED_PEAK - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.ChIPSeqDataFormats: Gapped peak format.
GENE_EST_ONLY - fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode
generalConf(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.Infos: Return a list with general configuration informations.
generateConditionPart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Add condition vector to R script.
generateExpressionFileNamesPart(StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Add expression file name vector to R script.
generateRepTechGroupPart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Write the section of the script that handle technical replicate groups.
generateRnwpreamble(List<Sample>, String, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Write Rnw preamble.
generateSampleIdsPart(List<Integer>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Add SampleIds vector to R script.
generateSampleNamePart(List<String>, StringBuilder) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Add sampleNames vector to R script.
generateScript(Experiment, TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna
generateScript(Experiment, TaskContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.Normalization: Generate the R script.
Generator - Annotation Type in fr.ens.biologie.genomique.eoulsan.annotations: This annotation is used to mark a step class that is a generator with user custom parameters.
GENERATOR_STEP - fr.ens.biologie.genomique.eoulsan.core.Step.StepType
GenericExecutorInterpreter - Class in fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters: This class define a generic executor interpreter.
GenericExecutorInterpreter(String) - Constructor for class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter: Constructor.
GenericStorageGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This module allow to easily store output of generator to avoid computation at each Eoulsan startup.
GenericStorageGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
GENOME_DESC_TXT - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Genome data format.
GENOME_DESCRIPTION - Static variable in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
GENOME_DESCRIPTION_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
GENOME_DESCRIPTION_PORT_NAME - Static variable in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
GENOME_FASTA - Static variable in class fr.ens.biologie.genomique.eoulsan.data.DataFormats: Genome data format.
GENOME_FILE_KEY - Static variable in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata
GenomeChecker - Class in fr.ens.biologie.genomique.eoulsan.checkers: This class define a Checker on genome FASTA files.
GenomeChecker() - Constructor for class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
GenomeDataProtocol - Class in fr.ens.biologie.genomique.eoulsan.data.protocols: This class define a genome protocol.
GenomeDataProtocol() - Constructor for class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
GenomeDescriptionCreator - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class define a genome description creator.
GenomeDescriptionCreator() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionCreator: Public constructor.
GenomeDescriptionGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class implements a genome description generator module.
GenomeDescriptionGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
GenomeMapperIndexGeneratorModule - Class in fr.ens.biologie.genomique.eoulsan.modules.generators: This class define a module that generate a genome mapper index.
GenomeMapperIndexGeneratorModule() - Constructor for class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
get(Parameter) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.SizeFactorsType: Get the size factors type to be used in DESeq2.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Get some data.
get(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the value of metadata entry.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
get(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the value according the key.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
get(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.FitType: Get the fit type to be used in DESeq2.
get(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2.StatisticTest: Get the statistic test to be used in DESeq2.
get(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo: Get the value for a key
getAction() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the action.
getActionArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the action arguments.
getActions() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService: Get the list of actions available.
getAdditionalAnnotationFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Get the additional annotation file.
getAdditionalAnnotationFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
getAdditionalAnnotationHypertextLinksPath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the additional annotation hypertext links path.
getAdditionalAnnotationStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the additional annotation storage path.
getAlias() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the alias of the name of the format.
getAlias() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getAlias() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getAlignmentFilter(GenericLogger, ReporterIncrementer, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule: Get the ReadAlignmentsFilter object.
getAlignmentsFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the parameters of the read alignments filters.
getAlignmentsFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule: Get the parameters of the alignments filter.
getAllDefaultStepId() - Static method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType: Return the available default step ids of the step types.
getAllFiles(File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get all the file on the Rserve server.
getAllFormats() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get all the registered formats.
getAllModules() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry: Get all the modules.
getAllSamplesMetadataKeys(Design) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get all the sample metadata keys of the samples of a design.
getAnnotationClass() - Method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Get the Eoulsan annotation class that corresponds to the Eoulsan mode.
getArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get command line arguments.
getArgv0() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
getAsBoolean(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the value according the key as a boolean.
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getAsBoolean(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.AbstractMetadata
getAsList(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Metadata: Get the value according the key as a list.
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getAsList(String) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get Author.
getAWSAccessKey() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the AWS access key.
getAWSSecretKey() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the AWS secret key.
getBasename() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the base name of this DataFile without all its extensions.
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
getBasePath() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol: Get the path where searching the files.
getBogoMips() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get processor bogomips.
getBooleanSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the value of the setting as a boolean value
getBooleanValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a boolean value.
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BpipeTaskScheduler: Get the path to the Bpipe command wrapper.
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler
getBpipeCommandWrapper() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
getBytesNumberWritten() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountOutputStream: Get the number of bytes written.
getBytesRead() - Method in class fr.ens.biologie.genomique.eoulsan.io.ByteCountInputStream: Get the number of bytes read.
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the checker for the module
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get Checker.
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getChecker() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the checker needed to check data of this type.
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getChecker() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getCheckersRequired() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Get the list of Checker required to run before this checker.
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
getCheckersRequired() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
getCheckerStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow: Get checker step.
getCheckStore() - Static method in class fr.ens.biologie.genomique.eoulsan.checkers.CheckStore: Get the instance of the CheckStore.
getCheetahScript() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the Cheetah script.
getClassPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get Eoulsan classpath.
getClusterSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the name of the cluster scheduler.
getCommandAuthor() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the command author.
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getCommandAuthor() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the command author.
getCommandDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get command description.
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getCommandDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get command description.
getCommandLine() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Get the context command line.
getCommandLine() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getCommandLine() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Gets the command line as a list of string arguments.
getCommandLineAsString() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Gets the command line as a String.
getCommandLineSettings() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the command line settings arguments.
getCommandName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the command name.
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getCommandName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the command name.
getComment() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the comment.
getComparisons() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the comparisons DEseq2 option.
getComparisons() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getCompression() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the compression.
getCompression() - Method in interface fr.ens.biologie.genomique.eoulsan.core.OutputPort: Get the compression format of the port.
getCompression() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleOutputPort
getCompressionExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the compression extension of this DataFile.
getCompressionLevel() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule: Get the compression level to use.
getCompressionsAccepted() - Method in interface fr.ens.biologie.genomique.eoulsan.core.InputPort: Test if the port accept a compressed input format.
getCompressionsAccepted() - Method in class fr.ens.biologie.genomique.eoulsan.core.SimpleInputPort
getCompressionType() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the compression Type of this DataFile.
getCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Get the condition.
getCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
getCondition() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the condition.
getCondition() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getCondition(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the Condition metadata value for an experimentSample.
getCondition(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the Condition metadata value for an experimentSample.
getConf() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
getConfiguration() - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime: Get Hadoop configuration.
getConfiguration(JobContext) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil: Invoke getConfiguration() method on JobContext.
getConfigurationFileArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the configuration file argument.
getConfigurationFilePath() - Static method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the configuration file path.
getContentEncoding() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the content type of the file.
getContentLength() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the content length of the file.
getContentLength() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getContentMD5() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the content MD5 of the file.
getContentType() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the content type of the file.
getContentType() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the content type.
getContentType() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getContentType() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getContextCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TokenManager: Get the number of context created by the token manager.
getContextCounters(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the contextName counters.
getContextCreationTime() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the creation time of the context.
getContextCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getContextCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the creation time of the context.
getContextId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the context id.
getContextMessage(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get a context message.
getContextName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the context name.
getContextName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getContextName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the context name.
getContrastFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the contrastFile DEseq2 option.
getContrastFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getCores() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get the number of cores of the processor.
getCount() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.fastqc.CounterSequenceFile: Get the count of the read entries.
getCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
getCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
getCounter(TaskInputOutputContext, String, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.ContextUtil
getCounterFromEoulsanName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Get an counter from its HTSeq-count name
getCounterFromHTSeqCountName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionCounterCounter: Get an counter from its HTSeq-count name
getCounterGroup() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the counter group to use for this module.
getCounterGroups() - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
getCounterNames(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
getCounters() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Get the sample counters.
getCounters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getCounterValue(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.HadoopReporter
getCPUMHz() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get CPU MHz.
getCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the creation time of the job.
getCreationTime() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
getCurrentKey() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
getCurrentStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the current step.
getCurrentStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getCurrentStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
getCurrentValue() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
getData(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Create an InputStream from the source.
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
getData(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the file as a DataFile.
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFile() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the DataFile for an input DataType and a Sample.
getDataFile() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getDataFile(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFile(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFile(int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the DataFile for an input DataType and a Sample.
getDataFile(MapperInstance, GenomeDescription, Map<String, String>) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage: Get the DataFile that corresponds to a mapper and a genome
getDataFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage: Get a Datafile related to a short name
getDataFileCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFileCount() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFileCount() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Count the number for DataFile available for a multi-file DataFormat and a Sample.
getDataFileCount(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFileCount(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFileCount(boolean) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Count the number for DataFile available for a multi-file DataFormat and a Sample.
getDataFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFilename() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFilename() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the pathname for the data.
getDataFilename(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getDataFilename(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getDataFilename(int) - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the pathname for the data.
getDataFileParent(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get the parent source of the source.
getDataFiles(Data) - Static method in class fr.ens.biologie.genomique.eoulsan.core.DataUtils: Get the list of the DataFile objects in a Data object.
getDataFiles(Data) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowDataUtils: Get the list of the DataFile objects in a Data object.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the DataFormat of the DataFile.
getDataFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the DataFormat of the file.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.DataToolElement: Get the data format of the tool element.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
getDataFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessor: Get the DataFormat handled by the preprocessor.
getDataFormat() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
getDataFormatForDesignMetadata(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the DataFormat that define a metadata entry in the design file.
getDataFormatForSampleMetadata(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the DataFormat that define a metadata entry of a sample in the design file.
getDataFormatFromAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat from its alias.
getDataFormatFromFilename(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the DataFormat of a file from its filename
getDataFormatFromFilename(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat From a file prefix and extension
getDataFormatFromGalaxyFormatName(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get DataFormat from an Galaxy format name.
getDataFormatFromGalaxyFormatNameOrNameOrAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat from its Galaxy format name or its name or alias.
getDataFormatFromName(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat from its name.
getDataFormatFromNameOrAlias(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get a DataFormat from its alias.
getDataFormatPaths() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the format paths.
getDataFormatsFromExtension(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get DataFormats from an extension.
getDataName() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the data name.
getDataPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the data directory path.
getDataRepositoryDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the data repository directory.
getDataRepositoryDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the data repository directory.
getDate() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the date.
getDefaultClusterMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the default memory required for the steps in cluster mode.
getDefaultExtension() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the default extension of the DataType.
getDefaultExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getDefaultExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getDefaultFastqFormat() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the default fastq format.
getDefaultProtocol() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService: Get the default protocol.
getDefaultStepId() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType: Get default step id.
getDefaultWorkFile(TaskAttemptContext, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.AbstractInfoAction
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Get action description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the description of the module
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskStatus: Get the context description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the description of the format.
getDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the tool description.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: A short description of the tool and what is done in the step.
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
getDescription() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the design used by the workflow.
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the design related to the experiment.
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getDesign() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the design related to the sample.
getDesign() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getDesign(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignBuilder: Create design object.
getDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the design file path.
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the design file.
getDesignFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the designFile DEseq2 option.
getDesignFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getDesignFormatVersion() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream: Get the format of the data to read.
getDesignMetadataKeyForDataFormat(Design, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the field name in a Design object that correspond to a dataformat.
getDesignMetadataKeyName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the name of the design metadata key of the design file that can provide the DataFile.
getDesignMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getDesignMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getDesignPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the design file path.
getDesignReader() - Method in class fr.ens.biologie.genomique.eoulsan.design.io.DesignFormatFinderInputStream: Get the DesignReader for the data.
getDesignStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getDesignStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the design step of the workflow.
getDest() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
getDiscardOutput() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get the discard output value.
getDispEstFitTypeFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType: Get the Dispersion estimation fit type form its name
getDispEstMethodFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod: Get the Dispersion estimation method form its name
getDispEstSharingModeFromName(String) - Static method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode: Get the Dispersion estimation sharing mode form its name
getDockerBackend() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Docker backend name.
getDockerConnection() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Docker connection string.
getDockerConnectionURI() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Docker connection URI.
getDockerImage() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get Docker image.
getDockerSingularityStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Docker singularity storage path.
getDoubleSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the value of the setting as a double value
getDoubleValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a double value.
getDuration() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult: Get the duration of the step.
getDuration() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the duration of the step.
getDuration() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
getEoulsanDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get Eoulsan directory.
getEoulsanMemory() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get Eoulsan memory requirement.
getEoulsanMode() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get the Eoulsan mode of the step.
getEoulsanScriptPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get Eoulsan script path.
getErrorMessage() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult: Get the error message.
getErrorMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the error message.
getErrorMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
getException() - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskResult: Get the exception.
getException() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the exception.
getException() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskResultImpl
getException() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Gets the exception.
getExecutablePids(String) - Static method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils: Return a set withs pid of existing executable.
getExecutablesTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the temporary directory for executables.
getExecutablesTempDirectoryFile() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the temporary directory File for executables.
getExecutionMode(Class<?>) - Static method in enum fr.ens.biologie.genomique.eoulsan.annotations.ExecutionMode: Get the execution mode related to an annotation class.
getExitCode() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult: Return the exit code.
getExitValue() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolExecutorResult: Gets the exit value.
getExitValue() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult: Get the exit value of the process.
getExperiment(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the name of an experiment.
getExperiments() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the list of the experiments.
getExperimentSample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the experiment sample related to the sample.
getExperimentSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getExperimentSample(Sample) - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getExperimentSampleAllMetadataKeys(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get all the experiment metadata keys of the samples of a design.
getExperimentSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get experiment samples list.
getExperimentSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getExperimentSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getExperimentsUsingASample(Sample) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get all the experiments related to a sample.
getExpressionCounter() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule: Get the counter.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the extension of this DataFile without compression extension.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol: Get the file extensions of the files to search.
getExtension() - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader: Get the extension of the files to load.
getExtensions() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the extensions for the DataType
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol: Get the list of the file extensions of the files to search.
getExtensions() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the FastqFormat.
getFastqFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the fastq format.
getFastqFormat(FastqFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the FastqFormat.
getFile() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
getFile() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
getFile(String) - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileStorage: Get a file related to a short name
getFile(String, File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get a file from the RServer.
getFileAsArray(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get a file as a byte array.
getFileIndex() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the file index.
getFileIndex() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get file index.
getFileInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Create an inputStream on a file on RServer.
getFileOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Create an outputStream on a file on RServer.
getFilesIntoZip(List<String>, File) - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get a list of files from the RServer.
getFirstPort() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
getFirstPort() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get the first port.
getFirstStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getFirstStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the first step of the workflow (after generator steps).
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Get format related to the checker.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the format.
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port: Get the data format of the port.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the format of the output
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the data format of the data.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMMerger
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.BAMSplitter
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionMerger
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.ExpressionSplitter
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqMerger
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.FastqSplitter
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Merger: Get the format related to the splitter.
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMMerger
getFormat() - Method in class fr.ens.biologie.genomique.eoulsan.splitermergers.SAMSplitter
getFormat() - Method in interface fr.ens.biologie.genomique.eoulsan.splitermergers.Splitter: Get the format related to the splitter.
getFullExtension() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the base name of this DataFile with all its extensions (include compression extension).
getGalaxyFormatNames() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the extension from Galaxy tool file of the DataType.
getGalaxyFormatNames() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getGalaxyFormatNames() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getGalaxyToolPaths() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Galaxy tool path.
getGenerator() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the step needed to generate the DataType from DataTypes provided by the Design file.
getGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getGenerator() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getGenericLogger() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the generic logger.
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getGenericLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the generic logger.
getGenericLogger() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger
getGenomeDescStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the genome description storage path.
getGenomeFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Get the genome file.
getGenomeFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
getGenomeMapperIndexStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the genome mapper index storage path.
getGenomeStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the genome storage path.
getGffFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Get the GFF file.
getGffFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
getGFFStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the GFF storage path.
getGlobalParameters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the globals parameters.
getGtfFile() - Method in interface fr.ens.biologie.genomique.eoulsan.design.DesignMetadata: Get the GTF file.
getGtfFile() - Method in class fr.ens.biologie.genomique.eoulsan.design.DesignMetadataImpl
getGTFStoragePath() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the GTF storage path.
getHadoopLogLevel() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the Hadoop log level.
getHadoopWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the Hadoop working directory.
getHadoopWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the local working directory.
getHadoopWorkingDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the Hadoop working directory.
getHadoopWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the Hadoop working path.
getHadoopWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the Hadoop working directory.
getHelp() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Gets the help.
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the command used to launch Eoulsan.
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
getHelpEoulsanCommand() - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get step id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: get the experiment id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getId() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the sample id.
getId() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxInfo: Get the file to parse.
getInfoFile() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxMemInfo
getInputData(InputPort) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get raw access to input data stored in the object.
getInputData(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the input data for an input DataType and a Sample.
getInputData(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getInputData(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the input data for a port name and a Sample.
getInputData(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getInputDataElements() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the in data format expected associated with variable found in command line.
getInputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the input data format.
getInputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the input ports of the step.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Define input port.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Define input ports.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Define input ports.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Define input port.
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.hadoop.ExpressionHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.FilterAndMapReadsHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsFilterHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.ReadsMapperHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAM2BAMHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.SAMFilterHadoopModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getInputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
getInputs() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the inputs.
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create an InputStream to load data.
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService: Retrieve the singleton static instance of an ActionService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService: Retrieve the singleton static instance of an ClusterTaskSchedulerService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.EmergencyStopTasks: Get the singleton instance of the class.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleRegistry: Retrieve the singleton static instance of ModuleRegistry.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances: Singleton method.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepObserverRegistry: Get the singleton instance of WorkflowStepObserverRegistry.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowEventBus: Get the singleton instance of WorkflowBusEvent.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the singleton instance of DataFormatRegistry
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService: Retrieve the singleton static instance of DataProtocolService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.Main: Get the instance of the Main class.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService: Retrieve the singleton static instance of an AlignmentsFilter.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService: Retrieve the singleton static instance of a RequirementService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.ui.UIService: Retrieve the singleton static instance of UIService.
getInstance() - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanDockerManager: Get the instance of the DockerManager.
getInstance(DataFile) - Static method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage: Get the singleton.
getInstance(DataFile, GenericLogger) - Static method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeDescStorage: Create a GenomeDescStorage
getInstance(String, GenericLogger) - Static method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileGenomeIndexStorage: Create a GenomeIndexStorage
getInterpreter(boolean) - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.ToolInfo: Get the interpreter.
getInterpreterPath() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter: Get the interpreter path.
getIntSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the value of the setting as a integer value
getIntValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a integer value.
getIntValueGreaterOrEqualsTo(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: * Get the value of the parameter as a integer value and check if this value is greater or equals to the min parameter value.
getIntValueInRange(int, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a integer value and check if this value is in the correct range.
getJarFile() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the application jar file.
getJarPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the application jar file.
getJarPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the application jar path.
getJarPathname(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the application jar file.
getJavaExecutablePath() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get java executable path.
getJavaMailSMTPProperties() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Create a property object for javamail smtp configuration from the settings.
getJobDescription() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the job description.
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the job description.
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobDescription() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the job description.
getJobDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the job path.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the job directory.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the job directory.
getJobDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the job path.
getJobDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the job directory.
getJobEnvironment() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the job environment.
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the job environment.
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobEnvironment() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the job environment.
getJobHost() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the host of the job.
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobHost() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the host of the job.
getJobId() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the job id.
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the job id.
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobId() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the job id.
getJobPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the job path.
getJobUUID() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the UUID of the job.
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getJobUUID() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the UUID of the job.
getJVMArgs() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get JVM arguments.
getJVMsPIDs() - Static method in class fr.ens.biologie.genomique.eoulsan.util.locker.LockerUtils: Return a set withs pid of existing JVMs.
getLabel() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Gets the label.
getLastActiveTime() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getLastModified() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the date of the last modification of the file.
getLastModified() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getLaunchMode() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the launch mode of the application.
getLaunchScriptPath() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the path to the launch script.
getLinkedSteps() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
getLinkedSteps() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port: Get the steps linked to this port.
getLinksFileFromSettings(Settings) - Static method in class fr.ens.biologie.genomique.eoulsan.util.EoulsanTranslatorUtils: Get the links file from the settings.
getLinkTarget() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFileMetadata: Get the symbolic link target.
getListElements() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getListElements() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getListElements() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the the list of data.
getLocalTempDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get local temporary directory.
getLocalTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getLocalTempDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getLocalThreadsNumber() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the number of threads to use in Steps computation in local mode.
getLocalWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl: Get the local working directory.
getLocalWorkingDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the local working directory.
getLocalWorkingDirectory(TaskContext) - Static method in class fr.ens.biologie.genomique.eoulsan.core.ContextUtils: Get the local working directory.
getLocalWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the local working path.
getLocalWorkingPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl: Get the local working directory.
getLogFileArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the log file argument.
getLogger() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the logger.
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getLogger() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the logger.
getLogger() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Get the logger object.
getLoggerName() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanLogger: Get the logger name.
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the Handler to create the log file.
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.MainCLI
getLogHandler(URI) - Method in class fr.ens.biologie.genomique.eoulsan.MainHadoop
getLogLevelArgument() - Method in class fr.ens.biologie.genomique.eoulsan.Main: Get the log level arguments.
getLowerStringValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the value of the parameter as a lower case String value.
getMapKey(Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule: Define the key to use for replicate merging.
getMapKey(Data) - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
getMapper() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the mapper.
getMapper() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the mapper object.
getMapperArguments() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the name of the mapper to use.
getMapperArguments() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the arguments of the mapper to use.
getMapperDockerImage() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the mapper Docker image to use.
getMapperFlavor() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the flavor of the mapper to use.
getMapperFlavor() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the flavor of the mapper to use.
getMapperHadoopMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the amount in MB of memory required to execute the mapper.
getMapperHadoopMemoryRequired() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the amount in MB of memory required to execute the mapper.
getMapperHadoopThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the name of the mapper to use.
getMapperHadoopThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the number of threads to use in local mode.
getMapperLocalThreads() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the number of threads to use in local mode.
getMapperName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the name of the mapper to use.
getMapperName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the name of the mapper to use.
getMapperVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the version of the mapper to use.
getMapperVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the version of the mapper to use.
getMaxFilesCount() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the maximal number of files used to store data of this format.
getMaxFilesCount() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getMaxFilesCount() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getMaxRecordsInRam() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule: Get the maximum records in RAM.
getMemTotal() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxMemInfo: Get the total memory of the system.
getMergeableWorkFile(Path, String, String, TaskAttemptContext, String) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils: Returns a name that mergeInto() will recognize as a file to be merged.
getMerger() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the merger class related to this type.
getMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getMerger() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIWorkflowEvent: Get the message of the event.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get metadata about the data.
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the design Metadata.
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the experiment metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSample: Get the experiment sample metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
getMetadata() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the sample metadata.
getMetadata() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataMetadataStorage: Get the metadata of a file.
getMetadata(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get the metadata for the source.
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DeprecatedDataProtocol
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
getMetadata(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.URLDataProtocol
getMetadata(Experiment, Sample, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get a metadata value for an experiment and a sample.
getMetadata(ExperimentSample, String) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get a metadata value for an experimentSample.
getMetaData() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the metadata for this DataFile.
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ActionService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskSchedulerService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ModuleService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessorService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RequirementService
getMethodName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.UIService
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Get Eoulsan mode.
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getMode() - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getModel() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the model DEseq2 option.
getModel() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getModelColumns(Experiment) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the column names used in DESeq2 model.
getModelName() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get the model of processor
getModule() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get the underlying Module object.
getModule(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances: Get a module instance.
getModule(Step, String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepInstances: Get a step instance.
getModuleName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the module name.
getModuleName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getModuleName(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the module name of the step.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.actions.Action: Get the name of the action.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterExecAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ClusterTaskAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateDesignAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.CreateHadoopJarAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ExecJarHadoopAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.FormatsAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.HadoopExecAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.InfoAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.IntegrationTestAction
getName() - Method in class fr.ens.biologie.genomique.eoulsan.actions.ModulesAction
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.checkers.Checker: Get the name of the checker.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.DESeq2DesignChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GenomeChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GFFChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.GTFChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.checkers.ReadsChecker
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPort
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the name of the module.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.Parameter: Get the name of the parameter.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Port: Get the name of the port.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get data name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the name of this DataFile.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the name of the format.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AdditionalAnnotationDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.AnnotationDataProtocol
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get Protocol name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPPathDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FTPURLDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GenomeDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GFFDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.GTFDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HDFSPathDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPPathDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSPathDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPSURLDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.HTTPURLDataProtocol
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get design name.
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the experiment name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the sample name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement: Gets the name.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DefaultExecutorInterpreter
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.DockerExecutorInterpreter
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.ExecutorInterpreter: Get the name of the interpreter.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.executorinterpreters.GenericExecutorInterpreter
getName() - Method in class fr.ens.biologie.genomique.eoulsan.Infos.Info: Get the name of the information
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CheckerModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule: Methods
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MergePeaksModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.CountSplicedReadsModule: Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.qc.IDRModule: Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Name of the Step.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.TrackHubModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionFitType: Get the dispersion estimation fitType name
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionMethod: Get the dispersion estimation method
getName() - Method in enum fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAna.DispersionSharingMode: Get the dispersion estimation sharingMode name
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FailModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FakeModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.FirstModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.CopyDesignAndWorkflowFilesToOutputModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.DefineDataFormatToDownload
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.HDFSDataDownloadModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.upload.UploadModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ShellModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TechnicalReplicateMergerModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.TerminalModule
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: The name of the requirement.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.BasicUI
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.LanternaUI
getName() - Method in class fr.ens.biologie.genomique.eoulsan.ui.NoUI
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.ui.UI: Get the name of the UI.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.DockerRExecutor
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.ProcessRExecutor
getName() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Get the name of the RExecutor.
getName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
getNote() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Get the note.
getNote() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the note.
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the unique numerical identifier of the step.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get design number.
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the experiment number.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Sample: Get the sample number.
getNumber() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getOperator() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the operator.
getOutputData(DataFormat, Data) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(DataFormat, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(DataFormat, String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for an input DataType and a Sample.
getOutputData(DataFormat, String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(String, Data) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for a port name and a Sample.
getOutputData(String, Data) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(String, String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for a port name and a Sample.
getOutputData(String, String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputData(String, String, int) - Method in interface fr.ens.biologie.genomique.eoulsan.core.TaskContext: Get the output data for a port name and a Sample.
getOutputData(String, String, int) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputDataElements() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the out data format expected associated with variable found in command line.
getOutputDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the output path.
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get the output directory.
getOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor: Get the output directory of the analysis.
getOutputFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.AbstractRExecutor
getOutputFiles() - Method in interface fr.ens.biologie.genomique.eoulsan.util.r.RExecutor: Get the output files of the analysis
getOutputFiles() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RserveRExecutor
getOutputPathname() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.ExecutorArguments: Get the output path.
getOutputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the output data format.
getOutputPorts() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the output ports of the step.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.MergeInputRepLocalModule: Define output port.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.RmDupLocalModule: Define output port.
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyInputDataModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.CopyOutputDataModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.AbstractExpressionModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastQCModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.DummyGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeDescriptionGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenomeMapperIndexGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GFFFastaGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.Minimap2IndexGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.STARIndexGeneratorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.ImportModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSplice2BEDModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.MergerModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.ExpressionToMatrixModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.MatrixToCellRangerMatrixModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getOutputPorts() - Method in class fr.ens.biologie.genomique.eoulsan.modules.SplitterModule
getOutputs() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.GalaxyToolInterpreter: Gets the outputs.
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create an OutputStream to load data.
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getOutputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getOutputTreeType() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the output tree type.
getParallelizationMode() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the parallelization mode of the module.
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep: Get the parallelization mode of the step.
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.DesignModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffanaResultsAnnotationModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.expression.ExpressionResultsAnnotationModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.local.ReadsMapperLocalModule
getParallelizationMode() - Method in class fr.ens.biologie.genomique.eoulsan.modules.RequirementInstallerModule
getParameter(Set<Parameter>, String) - Static method in class fr.ens.biologie.genomique.eoulsan.core.Modules: Get the last parameter which name match for a parameter set.
getParameters() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the parameter of the step.
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.AbstractRequirement
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.DockerRequirement
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.PathRequirement
getParameters() - Method in interface fr.ens.biologie.genomique.eoulsan.requirements.Requirement: Get the parameters of the requirement
getParameters() - Method in class fr.ens.biologie.genomique.eoulsan.requirements.RserveRequirement
getParent() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the parent of this DataFile.
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the file part.
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.DataList
getPart() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UnmodifiableData
getPart() - Method in interface fr.ens.biologie.genomique.eoulsan.data.Data: Get the part of the data.
getPath(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.PathDataProtocol: Get Convert a DataFile object to a Path object.
getPercentComplete() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.FastqSequenceFile
getPercentComplete() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.SAMSequenceFile
getPid() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.Ticket
getPort(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
getPort(String) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get a port.
getPortName() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the port name.
getPortName() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the port name that produced the file.
getPortNames() - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
getPortNames() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get the names of the ports
getPortsWithDataFormat(DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.core.AbstractPorts
getPortsWithDataFormat(DataFormat) - Method in interface fr.ens.biologie.genomique.eoulsan.core.Ports: Get a list with all the ports that format is the specified format.
getPrefix() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get DataFormat prefix.
getPrefix() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getPrefix() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getPriority() - Method in enum fr.ens.biologie.genomique.eoulsan.core.Step.StepType: Get the priority of the step.
getProcessesWaiting() - Method in class fr.ens.biologie.genomique.eoulsan.util.locker.ExecLock: Get the number of processes waiting.
getProcessor() - Method in class fr.ens.biologie.genomique.eoulsan.util.LinuxCpuInfo: Get the processor name.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqLineRecordReader: Get the progress within the split
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqRecordReader
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMRecordReader
getProgress() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress: Get the progress of the context processing.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStatus: Get the progress of the step.
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getProgress() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the progress.
getProgressMessage() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Progress: Get the progress message.
getProgressMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskStatusImpl
getProtocol() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the protocol of this DataFile.
getProtocolPrefixInSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the prefix of the protocol in the source name of the DataFile.
getRandomId() - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mgmt.hadoop.DistCp
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Create a raw InputStream (without decompression of input data) to load data.
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.HadoopEoulsanRuntime
getRawInputStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.LocalEoulsanRuntime
getRConnection() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get the R connection.
getReadFilter(GenericLogger, ReporterIncrementer, String) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule: Get the ReadFilter object.
getReadFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the parameters of the read filters.
getReadFilterParameters() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule: Get the parameters of the read filter.
getReads() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the reads as a list.
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.ExpressionOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.FastqOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.bio.io.hadoop.SAMOutputFormat
getRecordWriter(TaskAttemptContext) - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.CLIMergingAnySAMOutputFormat
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractBAM2SAMModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractFilterAndMapReadsModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsFilterModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractReadsMapperModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2BAMModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAM2FASTQModule: Get the reducer task count.
getReducerTaskCount() - Method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.AbstractSAMFilterModule: Get the reducer task count.
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentMetadata: Get the reference option.
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Get the reference.
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
getReference() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the reference.
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentMetadata
getReference() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getReference(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the reference of a sample.
getReference(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the reference of a sample.
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.ExpressionInputPreprocessor
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FastQCInputPreprocessor
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.FeatureCountsInputPreprocessor
getReportName() - Method in interface fr.ens.biologie.genomique.eoulsan.modules.multiqc.InputPreprocessor: Get the name of the report.
getReportName() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MapperInputPreprocessor
getRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadata: Get the RepTechGroup.
getRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleMetadataImpl
getRepTechGroup() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the RepTechGroup.
getRepTechGroup() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperimentSampleMetadata
getRepTechGroup(Experiment, Sample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the RepTechGroup metadata value for an experimentSample.
getRepTechGroup(ExperimentSample) - Static method in class fr.ens.biologie.genomique.eoulsan.design.DesignUtils: Get the Condition metadata value for an experimentSample.
getRequiredEoulsanVersion() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the required Version of the application to run the Module.
getRequiredEoulsanVersion() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getRequiredMemory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the required memory for the step.
getRequiredMemory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getRequiredProcessors() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the required processors for the step.
getRequiredProcessors() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getRequiredSteps() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies: Get the required steps.
getRequirements() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Module: Get the requirements of the module.
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.AbstractModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.BedToolsModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.DeepToolsModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.chipseq.peakcalling.MACS2Module
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DESeq2Module
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.DiffAnaModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.diffana.NormalizationModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.generators.GenericStorageGeneratorModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.multiqc.MultiQCModule
getRequirements() - Method in class fr.ens.biologie.genomique.eoulsan.modules.singlecell.RSingleCellExperimentCreatorModule
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader: Get the input stream related to a resource.
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.ClassPathResourceLoader
getResourceAsStream(String) - Method in class fr.ens.biologie.genomique.eoulsan.util.FileResourceLoader
getResourceName(S) - Method in class fr.ens.biologie.genomique.eoulsan.util.AbstractResourceLoader: Get the resource name.
getResult() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskRunner: Get the context result.
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getResult(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getResult(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the result related to a step.
getResultMail() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the mail address for eoulsan results.
getResultsPanel() - Method in class fr.ens.biologie.genomique.eoulsan.modules.fastqc.EmptyFileQC
getRootStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractWorkflow
getRootStep() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Workflow: Get the first steps of the workflow.
getRServeServerName() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the RServe server name.
getRuntime() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get EoulsanRuntime.
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getRuntime() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get EoulsanRuntime.
getRuntime() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanRuntime: Get the Eoulsan runtime instance.
getSAMHeaderMerger(Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.hadoopbamcli.Utils: Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
getSAMHeaderMerger(Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.modules.mapping.hadoop.HadoopBamUtils: Computes the merger of the SAM headers in the files listed in HEADERMERGER_INPUTS_PROPERTY.
getSample() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the sample that produced the file.
getSample() - Method in interface fr.ens.biologie.genomique.eoulsan.design.ExperimentSample: Get the experiment sample name.
getSample() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentSampleImpl
getSample(String) - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the name of a sample.
getSampleId() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the sample id related to the data.
getSampleMetadataKeyForDataFormat(Sample, DataFormat) - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFormatRegistry: Get the field name in a Sample object that correspond to a dataformat.
getSampleMetadataKeyName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the name of the sample metadata key of the design file that can provide the DataFile.
getSampleMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getSampleMetadataKeyName() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getSampleName() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the sample name related to the data.
getSampleNumber() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get the sample number related to the data.
getSampleNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataMetadata: Get the sample number related to the data.
getSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Design: Get the list of the samples.
getSamples() - Method in interface fr.ens.biologie.genomique.eoulsan.design.Experiment: Get the samples of the experiment.
getSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.ExperimentImpl
getSamples() - Method in class fr.ens.biologie.genomique.eoulsan.design.UnmodifiableExperiment
getScheduler() - Static method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskSchedulerFactory: Get the scheduler
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.BundledScriptBpipeTaskScheduler
getSchedulerName() - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler: Get the scheduler name.
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.DummyTaskScheduler
getSchedulerName() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.TGCCTaskScheduler
getSerialNumber() - Method in interface fr.ens.biologie.genomique.eoulsan.design.SampleMetadata: Get the serial number.
getServerName() - Method in class fr.ens.biologie.genomique.eoulsan.util.r.RSConnection: Get the name of the Rserve server.
getServiceClasses() - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocolService
getSetting(String) - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get a setting value.
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.AbstractEoulsanRuntime: Get Settings.
getSettings() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get Eoulsan settings.
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepConfigurationContextImpl
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.TaskContextImpl
getSettings() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.WorkflowContext: Get Eoulsan settings.
getSettings() - Static method in class fr.ens.biologie.genomique.eoulsan.EoulsanRuntime: Get instance settings.
getSettingsKeyToObfuscated() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get a set with the names of the settings to obfuscate.
getSettingsNames() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get a set of settings names.
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.AbstractToolElement: Gets the short name.
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ConditionalToolElement
getShortName() - Method in class fr.ens.biologie.genomique.eoulsan.galaxytools.elements.EmptyToolElement
getShortName() - Method in interface fr.ens.biologie.genomique.eoulsan.galaxytools.elements.ToolElement: Gets the short name.
getSize(Path, Configuration) - Static method in class fr.ens.biologie.genomique.eoulsan.util.hadoop.PathUtils: Get the length of a file.
getSMTPHost() - Method in class fr.ens.biologie.genomique.eoulsan.Settings: Get the name of the SMTP server host.
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.DataFile: Get the source of this DataFile.
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.data.storages.DataFileDataPath
getSource() - Method in class fr.ens.biologie.genomique.eoulsan.modules.GalaxyToolModule: Get the source the Galaxy tool.
getSourceAsFile(DataFile) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get the underlying File object for the DataFile if the protocol allow it.
getSourceAsFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.FileDataProtocol
getSourceAsFile(DataFile) - Method in class fr.ens.biologie.genomique.eoulsan.data.protocols.StorageDataProtocol
getSourceFilename(String) - Method in interface fr.ens.biologie.genomique.eoulsan.data.protocols.DataProtocol: Get the name of the filename that correspond to the source.
getSplitter() - Method in interface fr.ens.biologie.genomique.eoulsan.data.DataFormat: Get the splitter class related to this type.
getSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.MapperIndexDataFormat
getSplitter() - Method in class fr.ens.biologie.genomique.eoulsan.data.XMLDataFormat
getState() - Method in interface fr.ens.biologie.genomique.eoulsan.core.Step: Get the state of the step.
getState() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.AbstractStep
getState() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepStateDependencies: Get the state of the step.
getStatus() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the message type
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.ClusterCombinedTaskScheduler
getStatus(Step) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.CombinedTaskScheduler
getStatus(Step) - Method in interface fr.ens.biologie.genomique.eoulsan.core.schedulers.TaskScheduler: Get the status related to a step.
getStatusValue() - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.clusters.ClusterTaskScheduler.StatusResult: Get status value.
getStderr() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult: Get the standard error of the process
getStdout() - Method in class fr.ens.biologie.genomique.eoulsan.util.ProcessUtils.ProcessResult: Get the standard output of the process
getStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepOutputDataFile: Get the workflow step that produced the file.
getStep() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.UIStepEvent: Get the step.
getStep(int) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Get the step related to a context.
getStep(TaskContextImpl) - Method in class fr.ens.biologie.genomique.eoulsan.core.schedulers.AbstractTaskScheduler: Get the step related to a context.
getStepCounters() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get the step counters.
getStepDataProduct(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the data product for the step.
getStepDiscardOutput(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the discard output value.
getStepId() - Method in class fr.ens.biologie.genomique.eoulsan.core.FileNaming: Get Step Id.
getStepIds() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the list of step ids.
getStepInputs(String) - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.CommandWorkflowModel: Get the inputs of a step
getStepMessage() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.StepResult: Get step message.
getStepOutputDirectory() - Method in interface fr.ens.biologie.genomique.eoulsan.core.StepConfigurationContext: Get the step working directory.
getStepOutputDirectory() - Method in class fr.ens.biologie.genomique.eoulsan.core.workflow.