Index (Aozan 3.1.1 API)

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

A

ABOUT_TXT - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: About string, plain text version.
ABOUT_TXT - Static variable in class fr.ens.biologie.genomique.aozan.Globals: About string, plain text version.
AbstractFastqCollector - Class in fr.ens.biologie.genomique.aozan.collectors: The abstract class define commons methods for the Collectors which treats fastq files.
AbstractFastqCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector
AbstractFastQCSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define an abstract FastQC test.
AbstractFastQCSampleTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.AbstractFastQCSampleTest: Constructor that set the field of this abstract test.
AbstractGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a abstract Global test.
AbstractGlobalTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.AbstractGlobalTest: Constructor that set the field of this abstract test.
AbstractGlobalTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.AbstractGlobalTest: Constructor that set the field of this abstract test.
AbstractIlluminaDemuxDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define an abstract Illumina demultiplexing data processor.
AbstractIlluminaDemuxDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor
AbstractLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a abstract Lane test.
AbstractLaneTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest: Constructor that set the field of this abstract test.
AbstractLaneTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest: Constructor that set the field of this abstract test.
AbstractPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: This class define a abstract Global test.
AbstractPooledSampleTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest: Constructor that set the field of this abstract test.
AbstractPooledSampleTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest: Constructor that set the field of this abstract test.
AbstractProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: This class define a abstract Global test.
AbstractProjectTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest: Constructor that set the field of this abstract test.
AbstractProjectTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest: Constructor that set the field of this abstract test.
AbstractQCModuleAozan - Class in fr.ens.biologie.genomique.aozan.fastqc: This class replace normal class AbstracQCModule form
AbstractQCModuleAozan() - Constructor for class fr.ens.biologie.genomique.aozan.fastqc.AbstractQCModuleAozan
AbstractSampleSheetConverter - Class in fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter: This abstract class define a converter between a samplesheet in XLS format to CSV.
AbstractSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a abstract sample test.
AbstractSampleTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest: Constructor that set the field of this abstract test.
AbstractSampleTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest: Constructor that set the field of this abstract test.
AbstractSimpleGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a simple global test.
AbstractSimpleGlobalTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.AbstractSimpleGlobalTest: Constructor that set the field of this abstract test.
AbstractSimpleGlobalTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.AbstractSimpleGlobalTest: Constructor that set the field of this abstract test.
AbstractSimpleLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a simple lane test.
AbstractSimpleLaneTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest: Constructor that set the field of this abstract test.
AbstractSimpleLaneTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest: Constructor that set the field of this abstract test.
AbstractSimpleProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: This class define a simple lane test.
AbstractSimpleProjectTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest: Constructor that set the field of this abstract test.
AbstractSimpleProjectTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest: Constructor that set the field of this abstract test.
AbstractSimpleSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: This class define a simple lane test.
AbstractSimpleSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a simple sample test.
AbstractSimpleSampleTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest: Constructor that set the field of this abstract test.
AbstractSimpleSampleTest(String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest: Constructor that set the field of this abstract test.
AbstractSimpleSampleTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest: Constructor that set the field of this abstract test.
AbstractSimpleSampleTest(String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest: Constructor that set the field of this abstract test.
accept(DataType) - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.CategoryDataTypeFilter
accept(DataType) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.DataTypeFilter: Test if a data type is valid.
accept(DataType) - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.MultiDataTypeFilter
accept(DataType) - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.PartialDataTypeFilter
accept(DataType) - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.SimpleDataTypeFilter
accept(DataType) - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.TechnologyDataTypeFilter
accept(Class<?>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ActionService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessorService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProviderService
accept(Class<?>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.RunConfigurationProviderService
action(Configuration, List<String>, GenericLogger) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.action.Action: Execute action.
action(Configuration, List<String>, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.DoradoAction
action(Configuration, List<String>, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ExecAction
action(Configuration, List<String>, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.GuppyAction
action(Configuration, List<String>, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.LegacyAction
action(Configuration, List<String>, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ListAction
action(Configuration, List<String>, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.SampleSheetConvertAction
Action - Interface in fr.ens.biologie.genomique.aozan.aozan3.action: This interface define an action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.action.DoradoAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.action.ExecAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.action.GuppyAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.action.LegacyAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.action.ListAction: Name of this action.
ACTION_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.action.SampleSheetConvertAction: Name of this action.
ActionService - Class in fr.ens.biologie.genomique.aozan.aozan3.action: This class define a service to retrieve an Action.
ActionService() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.action.ActionService: Private constructor.
add(InputData) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Add all the content of an existing collection to the current collection
add(RunData) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Add a run data.
add(RunId) - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.RunIdStorage: Add a run id to the storage
add(String, DataStorage) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.DataStorageRegistry: Add a storage to the registry
add(Collection<RunData>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Add a run data.
addAlias(String, String) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.GenomeAliases: Add an alias.
addCommandLineArgument(List<String>, RunConfiguration, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor
addCommandLineArgument(List<String>, RunConfiguration, String, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor
addDataFileInRundata(File) - Method in class fr.ens.biologie.genomique.aozan.RunData: Add the data file in the rundata.
addDataFileInRundata(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Add the data file in the rundata.
addDataProvider(RunDataProvider) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Set an existing data provider
addDataProvider(String, String, boolean, Configuration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Add a data provider.
addEntity(int) - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.EntityStat: Adds the sample.
addExcludePattern(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.Tar: Add a pattern to exclude.
addFastqScreenReport(int, int, List<File>) - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector: Add a FastqScreen report.
addGenome(String, String) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult: Update the list of reference genome used by fastqscreen.
addIncludePattern(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.Tar: Add a pattern to exclude.
addIndex(int, String) - Method in class fr.ens.biologie.genomique.aozan.demux.ReDemux: Add an index to re-demultiplex.
additionalInit(RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor: Additional initialization.
additionalInit(RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
additionalInit(RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
addRunDataProjectEntries(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.EntityStat: Creates the run data project.
addSequencerName(String, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerNames: Add a sequencer.
addSequencersFromConfiguration(Configuration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerNames: Add sequencers in the aliases table from a configuration object.
addStep(Step) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Add a step.
addSteps(Collection<Step>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Add steps.
addStorage(String, DataStorage) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Add a storage.
addUnknownAlias(String) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.GenomeAliases: Add an alias.
addValues(Number) - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Add values in dataset.
ANALYZED - fr.ens.biologie.genomique.aozan.aozan3.DataType.Category
AOZAN_CONF_FILE_PATH - Static variable in class fr.ens.biologie.genomique.aozan.Settings
AOZAN_DEBUG_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Mode Aozan debug.
AOZAN_ENABLE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Aozan enable.
AOZAN_LOG_LEVEL_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Aozan log level.
AOZAN_LOG_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Aozan log path.
AOZAN_VAR_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Aozan directory var path.
Aozan2Compatibility - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This utility class contains methods for Aozan 2 code source compatibility.
Aozan2Compatibility() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2Compatibility
Aozan2Logger - Class in fr.ens.biologie.genomique.aozan
Aozan2Logger() - Constructor for class fr.ens.biologie.genomique.aozan.Aozan2Logger
Aozan2QCDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define an Aozan 2 QC data processor.
Aozan2QCDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2QCDataProcessor
Aozan3Exception - Exception in fr.ens.biologie.genomique.aozan.aozan3: This class define an Aozan exception
Aozan3Exception() - Constructor for exception fr.ens.biologie.genomique.aozan.aozan3.Aozan3Exception: Create a new Aozan3Exception.
Aozan3Exception(RunId, String) - Constructor for exception fr.ens.biologie.genomique.aozan.aozan3.Aozan3Exception: Create a new Aozan3Exception with a message.
Aozan3Exception(RunId, String, Throwable) - Constructor for exception fr.ens.biologie.genomique.aozan.aozan3.Aozan3Exception: Create a new Aozan3Exception with a message and a cause.
Aozan3Exception(RunId, Throwable) - Constructor for exception fr.ens.biologie.genomique.aozan.aozan3.Aozan3Exception: Create a new Aozan3Exception with a cause.
Aozan3Exception(String) - Constructor for exception fr.ens.biologie.genomique.aozan.aozan3.Aozan3Exception: Create a new Aozan3Exception with a message.
Aozan3Exception(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.aozan.aozan3.Aozan3Exception: Create a new Aozan3Exception with a message and a cause.
Aozan3Exception(Throwable) - Constructor for exception fr.ens.biologie.genomique.aozan.aozan3.Aozan3Exception: Create a new Aozan3Exception with a cause.
Aozan3Logger - Class in fr.ens.biologie.genomique.aozan.aozan3.log
AozanCollector - Class in fr.ens.biologie.genomique.aozan.collectors
AozanCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.AozanCollector
AozanException - Exception in fr.ens.biologie.genomique.aozan: A nestable Aozan exception.
AozanException() - Constructor for exception fr.ens.biologie.genomique.aozan.AozanException: Create a new AozanException.
AozanException(String) - Constructor for exception fr.ens.biologie.genomique.aozan.AozanException: Create a new AozanException with a message.
AozanException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.aozan.AozanException: Create a new AozanException with a message and a cause.
AozanException(Throwable) - Constructor for exception fr.ens.biologie.genomique.aozan.AozanException: Create a new AozanException from the message of another exception.
AozanLock - Class in fr.ens.biologie.genomique.aozan.aozan3.legacy: This class define a global lock for Aozan.
AozanLock(Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.legacy.AozanLock: Constructor.
AozanLoggerFactory - Class in fr.ens.biologie.genomique.aozan.aozan3.log: This class define a factory for loggers.
AozanRuntimeException - Exception in fr.ens.biologie.genomique.aozan: A nestable Aozan runtime exception.
AozanRuntimeException() - Constructor for exception fr.ens.biologie.genomique.aozan.AozanRuntimeException: Create a new AozanRuntimeException.
AozanRuntimeException(String) - Constructor for exception fr.ens.biologie.genomique.aozan.AozanRuntimeException: Create a new AozanRuntimeException with a message.
AozanRuntimeException(String, Throwable) - Constructor for exception fr.ens.biologie.genomique.aozan.AozanRuntimeException: Create a new AozanRuntimeException with a message and a cause.
AozanRuntimeException(Throwable) - Constructor for exception fr.ens.biologie.genomique.aozan.AozanRuntimeException: Create a new AozanRuntimeException with a cause.
AozanTest - Interface in fr.ens.biologie.genomique.aozan.tests: This interface define an Aozan QC test.
AozanTestRegistry - Class in fr.ens.biologie.genomique.aozan.tests: This class define a registry for Aozan tests.
AozanTestRegistry() - Constructor for class fr.ens.biologie.genomique.aozan.tests.AozanTestRegistry: Public constructor.
APP_BUILD_COMMIT - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The built commit of the application.
APP_BUILD_COMMIT - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The built commit of the application.
APP_BUILD_DATE - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The build date of the application.
APP_BUILD_DATE - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The build date of the application.
APP_BUILD_HOST - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The built host of the application.
APP_BUILD_HOST - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The built host of the application.
APP_BUILD_NUMBER - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The built number of the application.
APP_BUILD_NUMBER - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The built number of the application.
APP_BUILD_YEAR - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The build year of the application.
APP_BUILD_YEAR - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The build year of the application.
APP_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The name of the application.
APP_NAME - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The name of the application.
APP_NAME_LOWER_CASE - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The name of the application.
APP_NAME_LOWER_CASE - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The name of the application.
APP_VERSION - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The version of the application.
APP_VERSION - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The version of the application.
APP_VERSION_STRING - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The version of the application.
APP_VERSION_STRING - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The version of the application.
APPLICATION_CLASSPATH_JVM_ARG - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Main
APPLICATION_MEMORY - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Main
APPLICATION_PATH - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Main
APPLICATION_SCRIPT - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Main
AUTO - fr.ens.biologie.genomique.aozan.aozan3.util.UnTar.Compression
availableRuns() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Get available runs.
availableRuns(Collection<RunId>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Get available runs.

B

BasecallingModelSelector - Class in fr.ens.biologie.genomique.aozan.aozan3.nanopore: This class allow to select the model to use with Dorado from parameters like flowcell or kit references.
BasecallingModelSelector(Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Public constructor.
BaseCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a base count global test.
BaseCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.BaseCountGlobalTest: Public constructor.
BasePFMeanQualityScoreSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a percent quality mean score sample test.
BasePFMeanQualityScoreSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.BasePFMeanQualityScoreSampleTest: Public constructor.
BCL - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.DataType
BCL_CONVERT - fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput.Bcl2FastqVersion
BCL_CONVERT_FORBIDDEN_DATA_SECTION - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
BCL_DATA_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Aozan directory bcl path.
BCL_SPACE_FACTOR_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Aozan bcl space factor.
BCL2FASTQ_1 - fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput.Bcl2FastqVersion
BCL2FASTQ_2 - fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput.Bcl2FastqVersion
BCL2FASTQ_2_15 - fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput.Bcl2FastqVersion
BCL2FASTQ_ADAPTER_FASTA_FILE_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Blc2fastq adapter fasta file path.
BCL2FASTQ_ADDITIONNAL_ARGUMENTS_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Blc2fastq additionnal arguments.
BCL2FASTQ_COMPRESSION_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq compression fastq files.
BCL2FASTQ_COMPRESSION_LEVEL_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq compression level.
BCL2FASTQ_FASTQ_CLUSTER_COUNT_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq fastq cluster count.
BCL2FASTQ_MISMATCHES_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq mismatches.
BCL2FASTQ_OUTPUT_DIR - Static variable in class fr.ens.biologie.genomique.aozan.QC: Bcl2fastq output directory property key.
BCL2FASTQ_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq path.
BCL2FASTQ_USE_DOCKER_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Set available use container docker.
BCL2FASTQ_WITH_FAILED_READS_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq with failed reads.
Bcl2FastqIlluminaDemuxDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define an Illumina demultiplexing data processor that use bcl-convert.
Bcl2FastqIlluminaDemuxDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
Bcl2FastqOutput - Class in fr.ens.biologie.genomique.aozan.illumina: This class define the output of bcl2fastq.
Bcl2FastqOutput(SampleSheet, File) - Constructor for class fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput: Constructor.
Bcl2FastqOutput(SampleSheet, File, Bcl2FastqOutput.Bcl2FastqVersion, String, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput: Constructor.
Bcl2FastqOutput(File, File) - Constructor for class fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput: Constructor.
Bcl2FastqOutput.Bcl2FastqVersion - Enum in fr.ens.biologie.genomique.aozan.illumina: This enum defined the versions of bcl2fastq.
BclConvertIlluminaDemuxDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define an Illumina demultiplexing data processor that use bcl-convert.
BclConvertIlluminaDemuxDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
BlastContaminantHit - Class in fr.ens.biologie.genomique.aozan.fastqc: This class define a Blast contiminant Hit.
BlastContaminantHit(String) - Constructor for class fr.ens.biologie.genomique.aozan.fastqc.BlastContaminantHit
buildXMLCommonTagHeader(Document, Element, RunData) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsWriter: Add common tag in document header xml to describe Aozan and if data exists on run.
BZIP2 - fr.ens.biologie.genomique.aozan.aozan3.util.UnTar.Compression

C

cancelLogger() - Static method in class fr.ens.biologie.genomique.aozan.Common: Cancel logger.
canProvideRunData() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider
canProvideRunData() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider
canProvideRunData() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider
canProvideRunData() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProvider: Test if provider can provide RunData
CategoryDataTypeFilter - Class in fr.ens.biologie.genomique.aozan.aozan3.datatypefilter: This class define a DataTypeFilter that require a specific DataType.
CategoryDataTypeFilter(DataType.Category) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.CategoryDataTypeFilter: Consctructor.
changeDirectoryMode(Path, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.util.DiskUtils: Recursively change the mode of a directory.
changeDirectoryOwner(Path, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.util.DiskUtils: Recursively change the owner of a directory.
changeDirectoryOwner(Path, String, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.util.DiskUtils: Recursively change the owner of a directory.
changeSuperClassOverrepresentedModule(boolean) - Static method in class fr.ens.biologie.genomique.aozan.fastqc.RuntimePatchFastQC: Change superclass of Overrepresented Module from FastQC v0.11.2 to replace a new class, it add a link html to ncbi website in result table.
checkIfDirectory() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is a directory.
checkIfDirectory(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is a directory.
checkIfEnoughSpace(long) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Check if there is enough space on the storage for a required amount of disk space.
checkIfEnoughSpace(long, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Check if there is enough space on the storage for a required amount of disk space.
checkIfExists() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location exists.
checkIfExists(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location exists.
checkIfFile() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is a directory.
checkIfFile(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is a directory.
checkIfNotExists() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location not exists.
checkIfNotExists(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location not exists.
checkIfReadable() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is readable.
checkIfReadable(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is readable.
checkIfWritable() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is writable.
checkIfWritable(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is writable.
checkReadableDirectory(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is a readable directory.
checkReadableFile(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is a readable file.
checkRunId(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.IlluminaUtils: Check if the run id is valid.
checkSampleSheet(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter: Check the samplesheet.
checkSampleSheet(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.IlluminaSampleSheetConverter
checkSampleSheet(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.NanoporeSampleSheetConverter
checkType(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.DataType
checkWritableDirectory(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is a writable directory.
checkWritableFile(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Check if the data location is a writable file.
clear() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Clear the collection.
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Clear qc directory after successfully all FastqCollector.
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.AozanCollector
clear() - Method in interface fr.ens.biologie.genomique.aozan.collectors.Collector: Remove temporary files.
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.FastQCCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.ReadCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector
clear() - Method in class fr.ens.biologie.genomique.aozan.fastqc.OverrepresentedSequencesBlast: Clear sequences.
clearTemporaryFiles() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Delete all temporaries files (fastq tmp files and map files).
ClusterDensityGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: The class define test to compute the density cluster mean for the run.
ClusterDensityGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.ClusterDensityGlobalTest: Public constructor.
ClusterDensityLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a lane test on cluster density.
ClusterDensityLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityLaneTest: Public constructor.
ClusterDensityPFGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: The class define test to compute the density cluster mean passing filtre for the run.
ClusterDensityPFGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.ClusterDensityPFGlobalTest: Public constructor.
ClusterDensityPFLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a lane test on cluster density.
ClusterDensityPFLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityPFLaneTest: Public constructor.
ClusterRecoveryReportSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: The class adds in the qc report html a link to the report recoverable cluster results for each sample.
ClusterRecoveryReportSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.ClusterRecoveryReportSampleTest: Public constructor.
collect(QC) - Method in class fr.ens.biologie.genomique.aozan.RunDataGenerator: Collect data and return a RunData object.
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Collect data : browse data for call concrete collector.
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.AozanCollector
collect(RunData) - Method in interface fr.ens.biologie.genomique.aozan.collectors.Collector: Collect data.
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexStatsCollector
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.ErrorMetricsCollector: Collect data.
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.ExtractionMetricsCollector: Collect data from TileMetric interOpFile.
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector: Collect data from QualityMetric interOpFile.
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.TileMetricsCollector: Collect data from TileMetric interOpFile.
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.ReadCollector
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector
collect(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector
Collector - Interface in fr.ens.biologie.genomique.aozan.collectors: This interface define a Collector.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.AozanCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.FastQCCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector: Collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.interop.ErrorMetricsCollector: The sub-collector name from ReadCollector.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.interop.ExtractionMetricsCollector: The sub-collector name from ReadCollector.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector: The sub-collector name from ReadCollector.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.interop.TileMetricsCollector: The sub-collector name from ReadCollector.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.ReadCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector: The collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector: Collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector: Collector name.
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector
COLLECTOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector: The collector name.
COLLECTOR_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector: Collector prefix for updating rundata.
COLLECTOR_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector: Collector prefix for updating rundata
CollectorConfiguration - Class in fr.ens.biologie.genomique.aozan.collectors: This class define the configuration of a collector.
CollectorConfiguration(CollectorConfiguration) - Constructor for class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Public constructor.
CollectorConfiguration(Map<String, String>) - Constructor for class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Public constructor.
CollectorRegistry - Class in fr.ens.biologie.genomique.aozan.collectors: This class define a registry for Collectors.
CollectorRegistry() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.CollectorRegistry: Public constructor.
collectSample(RunData, FastqSample, File, boolean) - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Collect data for a fastqSample.
collectSample(RunData, FastqSample, File, boolean) - Method in class fr.ens.biologie.genomique.aozan.collectors.FastQCCollector
collectSample(RunData, FastqSample, File, boolean) - Method in class fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector
collectSample(RunData, FastqSample, File, boolean) - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector
collectSample(RunData, FastqSample, File, boolean) - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
Common - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define common methods for CLI.
Common - Class in fr.ens.biologie.genomique.aozan: This class contains common methods like logger initialization.
Common() - Constructor for class fr.ens.biologie.genomique.aozan.Common
compare(Integer, Integer) - Method in class fr.ens.biologie.genomique.aozan.RunData.PooledSampleComparator
compare(Integer, Integer) - Method in class fr.ens.biologie.genomique.aozan.RunData.ProjectComparator
compareTo(RecipeFinder.RecipePath) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder.RecipePath
computeQ30(long[]) - Static method in class fr.ens.biologie.genomique.aozan.util.MathUtils: Get the Q30 score from an array of longs with number of cluster for each quality score.
computeReport() - Method in class fr.ens.biologie.genomique.aozan.QC: Process data.
CONF_FILE_EXTENSION - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals
Configuration - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a configuration
Configuration() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Default constructor.
Configuration(Configuration) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Constructor.
ConfigurationDefaults - Class in fr.ens.biologie.genomique.aozan.aozan3: This class contains Configuration object defaults
ConfigurationXMLParser - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a XML parser for configuration.
ConfigurationXMLParser(String, String, Configuration, GenericLogger) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.recipe.ConfigurationXMLParser: Constructor.
configure(CollectorConfiguration, String) - Method in class fr.ens.biologie.genomique.aozan.fastqc.OverrepresentedSequencesBlast: Configure and check that Blastn can be launched.
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.AozanCollector
configure(QC, CollectorConfiguration) - Method in interface fr.ens.biologie.genomique.aozan.collectors.Collector: Configure the collector with the path of the run data.
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexStatsCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.FastQCCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.ReadCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector
configure(QC, CollectorConfiguration) - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
configure(TestConfiguration) - Method in interface fr.ens.biologie.genomique.aozan.tests.AozanTest: Configure the test.
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractSimpleGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.ClusterDensityGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.ClusterDensityPFGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.ErrorRateGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.OccupancyPercentGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.ProjectCountGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.Q30PercentGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.SampleCountGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.global.UndeterminedClusterPercentGlobalTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterPercentLaneTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhasingPrephasingPercentLaneTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhiXAlignPercentLaneTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhiXRawClusterCountLaneTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Q30PercentLaneTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldLaneTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldPFLaneTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenReportPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenSampleOvercontaminationCountPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.InProjectPercentPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.InRunPercentPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFBaseMeanQualityScorePooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFPercentPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.Q30PercentPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RecoverablePFClusterPercentPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RecoverableRawClusterPercentPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.SampleInPoolCountPooledSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.project.FastQScreenReportProjectTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.project.MultiQCReportProjectTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.project.RecoverablePFClusterPercentProjectTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.project.RecoverableRawClusterPercentProjectTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.BasePFMeanQualityScoreSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.ClusterRecoveryReportSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCAdapterContentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCBasicStatsSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCDuplicationLevelSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCKmerContentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCNContentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCOverrepresentedSequencesSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerBaseQualityScoresSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerBaseSequenceContentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerSequenceGCContentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerSequenceQualityScoresSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerTileSequenceQualitySampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCSequenceLengthDistributionSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenReportSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.InLanePercentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.PFPercentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.Q30PercentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverablePFClusterPercentSampleTest
configure(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverableRawClusterPercentSampleTest
configureDoubleInterval(TestConfiguration) - Method in class fr.ens.biologie.genomique.aozan.util.ScoreInterval
configureDoubleInterval(String, String) - Method in class fr.ens.biologie.genomique.aozan.util.ScoreInterval
configureLongInterval(String, String) - Method in class fr.ens.biologie.genomique.aozan.util.ScoreInterval
configureLongInterval(Map<String, String>) - Method in class fr.ens.biologie.genomique.aozan.util.ScoreInterval
contains(String) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.GenomeAliases
contains(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Test if the RunData contains a key.
contains(String) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Test if the line contains a field.
contains(String) - Method in class fr.ens.biologie.genomique.aozan.util.CVSParser: Test if the file contains a field
containsKey(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Test if configuration contains a key.
containsKey(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Test if the configuration contains a key.
containsKey(String) - Method in class fr.ens.biologie.genomique.aozan.Settings: Test if the settings contains a key.
containsKey(String) - Method in class fr.ens.biologie.genomique.aozan.tests.TestConfiguration: Test if the configuration contains a key.
ContaminantFinder - Class in fr.ens.biologie.genomique.aozan.fastqc: Source FastQC version 0.10.0, not modify.
ContaminantFinder() - Constructor for class fr.ens.biologie.genomique.aozan.fastqc.ContaminantFinder
convert() - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter: Convert the samplesheet.
CopyAndMergeGuppyOutput - Class in fr.ens.biologie.genomique.aozan.aozan3.util: Merge FASTQ files from a directory in another directory.
CopyAndMergeGuppyOutput(Path, Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Constructor.
countHitPerGenome(String, boolean, boolean) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult: Count for each read number of hit per reference genome.
countPercentValue(int, int) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult: Convert values from fastqscreen in percentage.
createDemuxCommandLine(Path, Path, Path, String, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor: Create the command line to execute the demultiplexing.
createDemuxCommandLine(Path, Path, Path, String, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
createDemuxCommandLine(Path, Path, Path, String, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
createGenomeDescription(File) - Method in class fr.ens.biologie.genomique.aozan.Storages: Create a GenomeDescription object from a Fasta file.
createHTMLFileFromXSL(File, File) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsWriter: Transform a XML file using XSL style sheet.
createHTMLFileFromXSL(String, String) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsWriter: Transform a XML file using XSL style sheet.
createHTMLFileFromXSL(Document, InputStream) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsWriter: Create a html file from document xml and xsl files.
createHTMLFileFromXSL(Document, InputStream, File) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsWriter: Create a html file from document xml and xsl files.
createIndexRun(Path, String, Collection<String>) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.IndexGenerator: Create index.html file in legacy mode.
createListFastqFiles() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Keep files that satisfy the specified filter in this directory and beginning with this prefix.
createListFastqSamples2(QC, RunData, boolean, boolean, boolean) - Static method in class fr.ens.biologie.genomique.aozan.io.FastqSampleUtils: Create a set of FastqSample to process.
createLock() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.AozanLock: Create the lock file.
createReport(File) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenProjectReport: Creates the HTML report.
createRundata(String) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult: Update rundata with results from fastqscreen.
createRunDataFile(File) - Method in class fr.ens.biologie.genomique.aozan.RunData: Create the data file.
createRunDataFile(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Create the data file.
createXMLFile(Document, File) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsWriter: Create a xml file from document xml.
createXMLFileContent(Document) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsWriter: Create a XML file content from XML document.
CSVLineParser - Class in fr.ens.biologie.genomique.aozan.util: This class define a line entry of a CSV file.
CVSParser - Class in fr.ens.biologie.genomique.aozan.util: This class allow to parse CSV files
CVSParser(Path) - Constructor for class fr.ens.biologie.genomique.aozan.util.CVSParser: Constructor.
CVSParser(Path, char) - Constructor for class fr.ens.biologie.genomique.aozan.util.CVSParser: Constructor.
CVSParser(List<String>) - Constructor for class fr.ens.biologie.genomique.aozan.util.CVSParser: Constructor.
CVSParser(List<String>, char) - Constructor for class fr.ens.biologie.genomique.aozan.util.CVSParser: Constructor.
Cycle100ErrorRateLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a test on error rate on 100 cycle.
Cycle100ErrorRateLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.Cycle100ErrorRateLaneTest: Public constructor.
Cycle20IntensityPercentLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a test on percent of intensity at cycle 20.
Cycle20IntensityPercentLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.Cycle20IntensityPercentLaneTest: Public constructor.
Cycle35ErrorRateLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a test on error rate on 35 cycle.
Cycle35ErrorRateLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.Cycle35ErrorRateLaneTest: Public constructor.
Cycle75ErrorRateLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a test on error rate on 75 cycle.
Cycle75ErrorRateLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.Cycle75ErrorRateLaneTest: Public constructor.
CycleCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a cycle count global test.
CycleCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.CycleCountGlobalTest: Public constructor.

D

DATA_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector
DataLocation - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a data location
DataLocation(DataStorage, Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Public constructor.
DataLocation.Format - Enum in fr.ens.biologie.genomique.aozan.aozan3: Format of the data location
DataProcessor - Interface in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This interface defines a data processor
DataProcessor.ProcessResult - Interface in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This interface define a process result
DataProcessorService - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define a service to retrieve a DataProcessor
DataProcessorService() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessorService: Private constructor.
DataProcessorTemplateEmailMessage - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define a template email message for end of step messages.
DataProcessorTemplateEmailMessage(Configuration, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessorTemplateEmailMessage: Public constructor.
DataStorage - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a data storage.
DataStorage(String, String) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Constructor.
DataStorage(String, String, SequencerSource) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Constructor.
DataStorage(String, Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Constructor.
DataStorage(String, Path, SequencerSource) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Constructor.
DataStorageRegistry - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a registry for data storages.
DataStorageRegistry() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.recipe.DataStorageRegistry
DataType - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a data type
DataType(DataType.Category, DataType.SequencingTechnology, String) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DataType
DataType(DataType.Category, DataType.SequencingTechnology, String, boolean, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DataType
DataType.Category - Enum in fr.ens.biologie.genomique.aozan.aozan3: Run data type.
DataType.SequencingTechnology - Enum in fr.ens.biologie.genomique.aozan.aozan3: Sequencing technology
DataTypeFilter - Interface in fr.ens.biologie.genomique.aozan.aozan3.datatypefilter: This interface define a filter for DataType.
debug(RunData, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log a debug message.
debug(RunId, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log a debug message.
debug(GenericLogger, RunData, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log a debug message.
debug(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log a debug message.
DEBUG - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: Set the debug mode.
DEBUG - Static variable in class fr.ens.biologie.genomique.aozan.Globals: Set the debug mode.
DEFAULT_FILE_ENCODING - Static variable in class fr.ens.biologie.genomique.aozan.Globals
DEFAULT_LOCALE - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: Default locale of the application.
DEFAULT_LOCALE - Static variable in class fr.ens.biologie.genomique.aozan.Globals: Default locale of the application.
DEFAULT_MAIL_FOOTER - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage
DEFAULT_MAIL_HEADER - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage
DEFAULT_SUBJECT_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage
DefaultRunIdGenerator - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define the default implementation of the RunIsGenerator interface.
DefaultRunIdGenerator() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DefaultRunIdGenerator: Constructor.
DefaultRunIdGenerator(String) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.DefaultRunIdGenerator: Constructor.
defineErrorFile(File, File) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter
defineOutputFile(File, File) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter
defineSampleSubDirName(String, String) - Static method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the sample sub directory.
defineWarningFile(File, File) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter
DemultiplexingCollector - Class in fr.ens.biologie.genomique.aozan.collectors
DemultiplexingCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector
DemultiplexStatsCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This collector parse Demultiplex_Stats.csv file generated by bcl-convert.
DemultiplexStatsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.DemultiplexStatsCollector
DEMUX_ARCHIVE_SAMPLESHEETS_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Archive samplesheets key.
DEMUX_SPACE_FACTOR_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Demultiplex space factor.
DEMUX_STEP_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Demultiplex step.
DEMUX_THREADS_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq threads.
DEMUX_USE_HISEQ_OUTPUT_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Demultiplex use Hiseq output.
DensityLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a density lane test.
DensityLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.DensityLaneTest: Public constructor.
description - Variable in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder.RecipePath
deSerializeFromJson(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Deserialize a DataStorage from JSON.
DIRECTORY - fr.ens.biologie.genomique.aozan.aozan3.DataLocation.Format
DiscoverNewIlluminaRunDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define an Illumina run discovering data processor.
DiscoverNewIlluminaRunDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DiscoverNewIlluminaRunDataProcessor
DiskUtils - Class in fr.ens.biologie.genomique.aozan.aozan3.util: This class contains some system utility methods.
DOCKER_URI_KEY - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.ConfigurationDefaults
DOCKER_URI_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Docker connection string.
doMap(File, File, List<String>, String, int) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenPseudoMapReduce: Mapper Receive value in SAM format, only the read mapped are added in output with reference genome.
doMap(File, List<String>, String, int) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenPseudoMapReduce: Mapper Receive value in SAM format, only the read mapped are added in output with reference genome.
DoradoAction - Class in fr.ens.biologie.genomique.aozan.aozan3.action: This class define an "dorado" action that will launch Dorado.
DoradoAction() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.action.DoradoAction
DoradoONTBasecallingDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class implements a Dorado data processor.
DoradoONTBasecallingDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor
DoubleInterval - Class in fr.ens.biologie.genomique.aozan.util: This class define a double interval.
DoubleInterval(double, boolean, double, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.util.DoubleInterval
DoubleInterval(double, double) - Constructor for class fr.ens.biologie.genomique.aozan.util.DoubleInterval
DoubleInterval(String) - Constructor for class fr.ens.biologie.genomique.aozan.util.DoubleInterval
du(Path) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.util.DiskUtils: This method returns the disk usage of a directory or a file.

E

EmailMessage - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define define an email message.
EmailMessage(long, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Constructor.
EmailMessage(long, String, String, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Constructor.
EmailMessage(String, String) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Constructor.
EMBEDDED_FASTQSCREEN_PROJECT_XSL - Static variable in class fr.ens.biologie.genomique.aozan.Globals
EMBEDDED_FASTQSCREEN_XSL - Static variable in class fr.ens.biologie.genomique.aozan.Globals
EMBEDDED_QC_XSL - Static variable in class fr.ens.biologie.genomique.aozan.Globals: Embedded XSL QC stylesheet.
EMBEDDED_UNDETERMINED_XSL - Static variable in class fr.ens.biologie.genomique.aozan.Globals
EmptyRunConfigurationProvider - Class in fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider: This class define an empty run configuration provider
EmptyRunConfigurationProvider() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.EmptyRunConfigurationProvider
EmptyRunDataProvider - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprovider: This class define an empty run data provider.
EmptyRunDataProvider() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider
endDataProcessorEmail(String, RunId, Path, long, long, long, long, Map<String, String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessorTemplateEmailMessage: Create an end of step message.
EndIlluminaRunDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define an Illumina end run data processor.
EndIlluminaRunDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.EndIlluminaRunDataProcessor
EntityStat - Class in fr.ens.biologie.genomique.aozan.collectors.stats: The class define a entity statistics which compute data collected on project, sample or others and update run data.
EntityStat(RunData, int, int, StatisticsCollector) - Constructor for class fr.ens.biologie.genomique.aozan.collectors.stats.EntityStat: Instantiates a new entity stat.
EntityStat(RunData, int, StatisticsCollector) - Constructor for class fr.ens.biologie.genomique.aozan.collectors.stats.EntityStat: Instantiates a new project stat.
entries() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Get all the entries in the collection
entrySet() - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get an entry set of the setting values.
entrySet() - Method in class fr.ens.biologie.genomique.aozan.Settings: Get an entry set of the setting values.
entrySet() - Method in class fr.ens.biologie.genomique.aozan.tests.TestConfiguration: Get an entry set of the setting values.
equals(Object) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType
equals(Object) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunId
equals(Object) - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.EntityStat
error(RunData, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(RunData, Throwable) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(RunId, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(RunId, Throwable) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(GenericLogger, RunData, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(GenericLogger, RunData, Throwable) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(GenericLogger, RunId, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(GenericLogger, RunId, Throwable) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
error(Throwable) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an error message.
errorExit(Throwable, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Common: Print error message to the user and exits the application.
errorExit(Throwable, String, boolean) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Common: Print error message to the user and exits the application.
errorExit(Throwable, String, boolean, int) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Common: Print error message to the user and exits the application.
errorExit(Throwable, String, int) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Common: Print error message to the user and exits the application.
errorFile - Variable in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter
errorMessage(Configuration, Throwable) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage
errorMessage(Throwable) - Method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Generate error EmailMessage object.
ErrorMetricsCollector - Class in fr.ens.biologie.genomique.aozan.collectors.interop: This class collects run data by reading the ErrorMetricsOut.bin in InterOp directory.
ErrorMetricsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.interop.ErrorMetricsCollector
ErrorRateGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: The class define test to compute the mean on the error rate phix for the run.
ErrorRateGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.ErrorRateGlobalTest: Public constructor.
ErrorRateLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a test on error rate.
ErrorRateLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.ErrorRateLaneTest: Public constructor.
ExecAction - Class in fr.ens.biologie.genomique.aozan.aozan3.action: This class define an exec action.
ExecAction() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.action.ExecAction
execute() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Use the recipe to process run provided by the run data provider
execute() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Execute the copy and merge FASTQ files.
execute() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.Tar: Execute tar.
execute() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.UnTar: Execute untar.
execute(File, File, String, List<String>, String, boolean) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreen: Mode single-end : execute fastqscreen.
execute(File, String, List<String>, String, boolean) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreen: Mode pair-end : execute fastqscreen.
execute(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Execute the recipe for a run.
execute(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Execute a list of run Ids.
exist() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Test if the data location exists.
exists() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Test if the data location exists.
exists(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.DataStorageRegistry: Test if a storage exists.
exit(int) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Common: Exit the application.
export(File) - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Export the QC report.
export(InputStream) - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Export the QC report.
ExternalTool - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define a class for calling external tool in DataProcessors.
extractEntityStats(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector: Extract entity stats.
extractEntityStats(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector
extractEntityStats(RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector
extractFirstValueToDouble(Document, String) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser
extractFirstValueToDouble(Element, String) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser
extractFirstValueToInt(Document, String) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser
extractFirstValueToInt(Element, String) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser
extractFirstValueToString(Document, String) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser
extractFirstValueToString(Element, String) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser
ExtractionMetricsCollector - Class in fr.ens.biologie.genomique.aozan.collectors.interop: This class collects run data by reading the ExtractionMetricsOut.bin in InterOp directory.
ExtractionMetricsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.interop.ExtractionMetricsCollector
extractValueToDouble(Document, String, int) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser: Return the first value at a specific index corresponding to the tag name in the document.
extractValueToDouble(Element, String, int) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser: Return the first value at a specific index corresponding to the tag name in the element.
extractValueToInt(Document, String, int) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser: Return the first value at a specific index corresponding to the tag name in the document.
extractValueToInt(Element, String, int) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser: Return the first value at a specific index corresponding to the tag name in the element.
extractValueToString(Document, String, int) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser: Return the first value at a specific index corresponding to the tag name in the document.
extractValueToString(Element, String, int) - Static method in class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser: Return the first value at a specific index corresponding to the tag name in the element.

F

FAST5_TAR - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.DataType
FASTQ_DATA_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Fastq directory data path.
FASTQ_EXTENSION - Static variable in class fr.ens.biologie.genomique.aozan.io.FastqSample: The Constant FASTQ_EXTENSION.
FASTQ_SPACE_FACTOR_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Fastq space factor.
FastQCAdapterContentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC per tile sequence quality module.
FastQCAdapterContentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCAdapterContentSampleTest: Public constructor.
FastQCBasicStatsSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC basic stats module.
FastQCBasicStatsSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCBasicStatsSampleTest: Public constructor.
FastQCCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This class define a FastQC Collector.
FastQCCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.FastQCCollector
FastQCDuplicationLevelSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC duplication level module.
FastQCDuplicationLevelSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCDuplicationLevelSampleTest: Public constructor.
FastQCKmerContentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC kmer content module.
FastQCKmerContentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCKmerContentSampleTest: Public constructor.
FastQCNContentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC N content module.
FastQCNContentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCNContentSampleTest: Public constructor.
FastQCOverrepresentedSequencesSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC over represented seqs module.
FastQCOverrepresentedSequencesSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCOverrepresentedSequencesSampleTest: Public constructor.
FastQCPerBaseQualityScoresSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC per base quality score module.
FastQCPerBaseQualityScoresSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerBaseQualityScoresSampleTest: Public constructor.
FastQCPerBaseSequenceContentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC per base sequence content module.
FastQCPerBaseSequenceContentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerBaseSequenceContentSampleTest: Public constructor.
FastQCPerSequenceGCContentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC basic stats module.
FastQCPerSequenceGCContentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerSequenceGCContentSampleTest: Public constructor.
FastQCPerSequenceQualityScoresSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC per sequence quality scores module.
FastQCPerSequenceQualityScoresSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerSequenceQualityScoresSampleTest: Public constructor.
FastQCPerTileSequenceQualitySampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC per tile sequence quality module.
FastQCPerTileSequenceQualitySampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerTileSequenceQualitySampleTest: Public constructor.
FastQCSequenceLengthDistributionSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample test for FastQC sequence length distribution module.
FastQCSequenceLengthDistributionSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQCSequenceLengthDistributionSampleTest: Public constructor.
FastqSample - Class in fr.ens.biologie.genomique.aozan.io: The class correspond of one entity to treat by AbstractFastqCollector, so a sample per lane and in mode-paired one FastSample for each read (R1 and R2).
FastqSample(Bcl2FastqOutput, File, String, int, int, int, String, String, String, String, String, boolean, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.io.FastqSample: Public constructor corresponding of a undetermined index sample.
FastqSample(Bcl2FastqOutput, File, String, int, int, Sample) - Constructor for class fr.ens.biologie.genomique.aozan.io.FastqSample: Public constructor (used only for tests)
FastqSample(QC, int, int, int) - Constructor for class fr.ens.biologie.genomique.aozan.io.FastqSample: Public constructor corresponding of a undetermined index sample.
FastqSample(QC, int, int, int, String, String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.io.FastqSample: Public constructor corresponding of a technical replica sample.
FastqSample(SampleSheet, File, File, String, int, int, int) - Constructor for class fr.ens.biologie.genomique.aozan.io.FastqSample: Public constructor corresponding of a undetermined index sample.
FastqSample(SampleSheet, File, File, String, int, int, int, String, String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.io.FastqSample: Public constructor corresponding of a technical replica sample.
FastqSampleUtils - Class in fr.ens.biologie.genomique.aozan.io
FastqScreen - Class in fr.ens.biologie.genomique.aozan.fastqscreen: This class execute fastqscreen pair-end mode or single-end.
FastqScreen(CollectorConfiguration) - Constructor for class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreen: Public constructor of fastqscreen.
FastqScreenCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This class manages the execution of Fastq Screen for a full run according to the properties defined in the configuration file Aozan, which define the list of references genomes.
FastqScreenCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector
FastqScreenGenomes - Class in fr.ens.biologie.genomique.aozan.fastqscreen: This class read the alias genome file.
FastqScreenGenomes(SampleSheet, String) - Constructor for class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenGenomes: Public constructor.
FastQScreenMappedExceptRefGenomeSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: The class adds in the qc report html one result from fastqScreen for each sample.
FastQScreenMappedExceptRefGenomeSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedExceptRefGenomeSampleTest: Public constructor.
FastQScreenMappedExceptRefPercentPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class adds in the qc report html one result from fastqScreen for each sample, after compile replicat data.
FastQScreenMappedExceptRefPercentPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest: Public constructor.
FastQScreenMappedPercentPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class add in the qc report html values from FastqScreen for each sample, after compile replica data and for each reference genomes.
FastQScreenMappedPercentPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest: Public constructor.
FastQScreenMappedPercentPooledSampleTest(String, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest: Public constructor, specific for a reference genome.
FastQScreenMappedPercentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: The class add in the qc report html values from FastqScreen for each sample and for each reference genomes.
FastQScreenMappedPercentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest: Public constructor.
FastQScreenMappedPercentSampleTest(String, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest: Public constructor, specific for a reference genome.
FastqScreenProjectReport - Class in fr.ens.biologie.genomique.aozan.fastqscreen: The class set a project HTML report file on detection contamination by compilation report on samples.
FastqScreenProjectReport(List<File>, String, File) - Constructor for class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenProjectReport: Instantiates a new fastq screen project report.
FastqScreenPseudoMapReduce - Class in fr.ens.biologie.genomique.aozan.fastqscreen: This class account reads that map to each of the reference genome.
FastqScreenPseudoMapReduce(File, boolean, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenPseudoMapReduce: Public construction.
FastQScreenReportPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample
FastQScreenReportPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenReportPooledSampleTest: Public constructor.
FastQScreenReportProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project
FastQScreenReportProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.FastQScreenReportProjectTest: Public constructor.
FastQScreenReportSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: The class adds in the qc report html a link to the report fastqScreen for each sample.
FastQScreenReportSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenReportSampleTest: Public constructor.
FastqScreenResult - Class in fr.ens.biologie.genomique.aozan.fastqscreen: This class manages results from fastqscreen.
FastqScreenSAMParser - Class in fr.ens.biologie.genomique.aozan.fastqscreen: This class ensures alignment fastqScreen treating the output format BAM of mapper.
FastqScreenSAMParser(File, String, boolean, GenomeDescription) - Constructor for class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenSAMParser: Initialize FastqScreenSAMParser : create the mapOutputFile and the list filters used for parsing SAM file.
FastQScreenSampleOvercontaminationCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes.
FastQScreenSampleOvercontaminationCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenSampleOvercontaminationCountPooledSampleTest: Public constructor.
FastQScreenSampleOvercontaminationCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define test on samples count on a project which exceed a contaminant threshold on percent mapped reads on dataset contaminants genomes.
FastQScreenSampleOvercontaminationCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.FastQScreenSampleOvercontaminationCountProjectTest: Public constructor.
fields() - Method in class fr.ens.biologie.genomique.aozan.util.CVSParser: Get the list of the fields.
FILE - fr.ens.biologie.genomique.aozan.aozan3.DataLocation.Format
FileUtils - Class in fr.ens.biologie.genomique.aozan.util: This class defines useful method to handle files.
filter(DataTypeFilter) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Filter the collection.
filterTests(Collection<String>) - Method in class fr.ens.biologie.genomique.aozan.QCReport: Filter test entry in the report
findContaminantHit(String) - Static method in class fr.ens.biologie.genomique.aozan.fastqc.ContaminantFinder
FIRST_BASE_REPORT_STEP_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: First base report step.
FirstCycleIntensityLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a test on first cycle intensity.
FirstCycleIntensityLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.FirstCycleIntensityLaneTest: Public constructor.
fixSampleSheet(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter: Fix the samplesheet.
fixSampleSheet(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.IlluminaSampleSheetConverter
fixSampleSheet(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.NanoporeSampleSheetConverter
FORK_VERSION_5 - Static variable in class fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector
FORK_VERSION_6 - Static variable in class fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector
FORK_VERSION_7 - Static variable in class fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector
fr.ens.biologie.genomique.aozan - package fr.ens.biologie.genomique.aozan: Root package of Aozan.
fr.ens.biologie.genomique.aozan.aozan3 - package fr.ens.biologie.genomique.aozan.aozan3
fr.ens.biologie.genomique.aozan.aozan3.action - package fr.ens.biologie.genomique.aozan.aozan3.action
fr.ens.biologie.genomique.aozan.aozan3.dataprocessor - package fr.ens.biologie.genomique.aozan.aozan3.dataprocessor
fr.ens.biologie.genomique.aozan.aozan3.dataprovider - package fr.ens.biologie.genomique.aozan.aozan3.dataprovider
fr.ens.biologie.genomique.aozan.aozan3.datatypefilter - package fr.ens.biologie.genomique.aozan.aozan3.datatypefilter
fr.ens.biologie.genomique.aozan.aozan3.legacy - package fr.ens.biologie.genomique.aozan.aozan3.legacy
fr.ens.biologie.genomique.aozan.aozan3.log - package fr.ens.biologie.genomique.aozan.aozan3.log
fr.ens.biologie.genomique.aozan.aozan3.nanopore - package fr.ens.biologie.genomique.aozan.aozan3.nanopore
fr.ens.biologie.genomique.aozan.aozan3.recipe - package fr.ens.biologie.genomique.aozan.aozan3.recipe
fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider - package fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider
fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter - package fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter
fr.ens.biologie.genomique.aozan.aozan3.util - package fr.ens.biologie.genomique.aozan.aozan3.util
fr.ens.biologie.genomique.aozan.collectors - package fr.ens.biologie.genomique.aozan.collectors: This package defines the collectors which collects data for a run.
fr.ens.biologie.genomique.aozan.collectors.interop - package fr.ens.biologie.genomique.aozan.collectors.interop: This package defines the collectors which collects data from InterOp binary files for a run.
fr.ens.biologie.genomique.aozan.collectors.stats - package fr.ens.biologie.genomique.aozan.collectors.stats: This package defines the statistics collectors which collects data for a run.
fr.ens.biologie.genomique.aozan.demux - package fr.ens.biologie.genomique.aozan.demux: This package allows to re-demultiplexing selected project sequencing.
fr.ens.biologie.genomique.aozan.fastqc - package fr.ens.biologie.genomique.aozan.fastqc: This package contains a QCModule for FastQC that list the bad tiles in a fastq file and class used for modify fastqc bytecode, it is necessary with FastQC version 0.10.1.
fr.ens.biologie.genomique.aozan.fastqscreen - package fr.ens.biologie.genomique.aozan.fastqscreen: This package contains a module fastqscreen for the contamination detection in each sample of a run.
fr.ens.biologie.genomique.aozan.illumina - package fr.ens.biologie.genomique.aozan.illumina: This package contains classes to handle files generated and used by Illumina software.
fr.ens.biologie.genomique.aozan.io - package fr.ens.biologie.genomique.aozan.io: This package contains general I/O classes for Aozan.
fr.ens.biologie.genomique.aozan.tests - package fr.ens.biologie.genomique.aozan.tests: This package contains class of tests which defines the collector to launch and creates a report of a quality control.
fr.ens.biologie.genomique.aozan.tests.global - package fr.ens.biologie.genomique.aozan.tests.global: This package contains class of global tests which defines the collector to launch and creates a report of a quality control.
fr.ens.biologie.genomique.aozan.tests.lane - package fr.ens.biologie.genomique.aozan.tests.lane: This package contains class of lane tests which defines the collector to launch and creates a report of a quality control.
fr.ens.biologie.genomique.aozan.tests.pooledsample - package fr.ens.biologie.genomique.aozan.tests.pooledsample: This package contains class of project tests which defines the collector to launch and creates a report of a quality control.
fr.ens.biologie.genomique.aozan.tests.project - package fr.ens.biologie.genomique.aozan.tests.project: This package contains class of project tests which defines the collector to launch and creates a report of a quality control.
fr.ens.biologie.genomique.aozan.tests.sample - package fr.ens.biologie.genomique.aozan.tests.sample: This package contains class of sample tests which defines the collector to launch and creates a report of a quality control.
fr.ens.biologie.genomique.aozan.util - package fr.ens.biologie.genomique.aozan.util: This package utility classes.

G

GenomeAliases - Class in fr.ens.biologie.genomique.aozan.fastqscreen: This class define a storage for genome name aliases.
GenomeNamesPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The Class GenomesProjectTest.
GenomeNamesPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.GenomeNamesPooledSampleTest: Public constructor.
GenomeNamesProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The Class GenomesProjectTest.
GenomeNamesProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.GenomeNamesProjectTest: Public constructor.
GenomeNamesSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a test to get the genome(s) reference(s) of a sample.
GenomeNamesSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.GenomeNamesSampleTest: Public constructor.
get(DataType) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Get the first RunData with a matching data type.
get(DataType.Category) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Get a RunData from its data type.
get(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get the value for a configuration key.
get(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.DataStorageRegistry: Get a data storage from its name
get(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a setting value.
get(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorRegistry: Get a Collector.
get(String) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.GenomeAliases: Return the reference genome corresponding to the genome sample if it is present in alias genomes file.
get(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a key.
get(String) - Method in class fr.ens.biologie.genomique.aozan.Settings: Get a setting value.
get(String) - Method in class fr.ens.biologie.genomique.aozan.tests.AozanTestRegistry: Get a the test instance.
get(String) - Method in class fr.ens.biologie.genomique.aozan.tests.TestConfiguration: Get a setting value.
get(String) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field.
get(String, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get the value for a configuration key.
get(String, String) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a setting value.
get(String, String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a key.
get(String, String) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field.
getAction() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the action.
getActionArgs() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the action arguments.
getActions() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ActionService: Get the list of actions available.
getAllPooledSamples() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get all samples ids (with undetermined samples) of the run.
getAllSamples() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get all samples identifiers (with undetermined samples) of the run.
getAllSamplesInLane(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get all samples names related to the lane as a list.
getAnalyzedSequenceCount() - Method in class fr.ens.biologie.genomique.aozan.fastqc.OverrepresentedSequencesBlast: Get the number of analyzed sequences
getApplicationClassPath() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the application classpath.
getApplicationDirectory() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the application directory.
getApplicationMemory() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the application memory requirement.
getApplicationScriptPath() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the application script path.
getArgs() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get command line arguments.
getAvalaibleRuns() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Get the list of available runs.
getBcl2FastqVersion() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the bcl2fastq version.
getBclDir() - Method in class fr.ens.biologie.genomique.aozan.QC: Get the BCL directory of the run.
getBoolean(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get a boolean configuration key.
getBoolean(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a setting value.
getBoolean(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a boolean key.
getBoolean(String, boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get a boolean value for a configuration key.
getBoolean(String, boolean) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a setting value.
getBoolean(String, boolean) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a boolean key.
getCategory() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Get the category of Data.
getChemistryType(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Get the chemistry type from the kit reference
getCollectorNames() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the list of collector names.
getCollectorPrefix() - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector: Gets the collector prefix.
getCollectorPrefix() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector
getCollectorPrefix() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.AozanCollector
getCollectorsNamesRequiered() - Method in interface fr.ens.biologie.genomique.aozan.collectors.Collector: Get the name of the collectors required to run this collector.
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector: Collectors to execute before fastqscreen Collector.
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.ReadCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector: Collectors to execute before fastqscreen Collector.
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
getCollectorsNamesRequiered() - Method in interface fr.ens.biologie.genomique.aozan.tests.AozanTest: Get the name of the collectors required for the test.
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.BaseCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.ClusterDensityGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.ClusterDensityPFGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.CycleCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.ErrorRateGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.LaneCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.LoadingConcentrationPercentGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanPFClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanPhiXRawClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanRawClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianPFClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianPhiXRawClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianRawClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.NonIndexedBaseCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.OccupancyPercentGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterPercentGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterSDGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXAlignPercentGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterSDGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.ProjectCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.Q30PercentGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.RawClusterCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.RawClusterSDGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.SampleCountGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.global.UndeterminedClusterPercentGlobalTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityPFLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle100ErrorRateLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle20IntensityPercentLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle35ErrorRateLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle75ErrorRateLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.DensityLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ErrorRateLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.FirstCycleIntensityLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.OccupancyPercentLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterCountLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterPercentLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhasingPrephasingPercentLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhiXAlignPercentLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhiXRawClusterCountLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Q30PercentLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.RawClusterCountLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldPFLaneTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenReportPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenSampleOvercontaminationCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.GenomeNamesPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.InProjectPercentPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.InRunPercentPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.IsIndexedPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.LaneCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MaxPFClusterCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MaxRawClusterCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MinPFClusterCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MinRawClusterCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFBaseMeanQualityScorePooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFClusterCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFClusterRecoveryCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFPercentPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.Q30PercentPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RawClusterCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RawClusterRecoveryCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RecoverablePFClusterPercentPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RecoverableRawClusterPercentPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.SampleCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.SampleInPoolCountPooledSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.FastQScreenReportProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.FastQScreenSampleOvercontaminationCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.GenomeNamesProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.IsIndexedProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.LaneCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MaxPFClusterCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MaxRawClusterCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MinPFClusterCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MinRawClusterCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MultiQCReportProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.PFClusterCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.RawClusterCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.RecoverablePFClusterPercentProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.RecoverableRawClusterPercentProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.project.SampleCountProjectTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractFastQCSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.BasePFMeanQualityScoreSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.ClusterRecoveryReportSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedExceptRefGenomeSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenReportSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.GenomeNamesSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.InLanePercentSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.PFClusterCountSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.PFPercentSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.Q30PercentSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RawClusterCountSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverablePFClusterCountSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverablePFClusterPercentSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverableRawClusterCountSampleTest
getCollectorsNamesRequiered() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverableRawClusterPercentSampleTest
getColumnName() - Method in interface fr.ens.biologie.genomique.aozan.tests.AozanTest: Get the column name of the test in the QC result file.
getColumnName() - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractGlobalTest
getColumnName() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest
getColumnName() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
getColumnName() - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest
getColumnName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest
getCompression() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.Tar: Get tar compression.
getCompression() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.UnTar: Get tar compression.
getCompressionType() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the compression type for fastq files.
getConfiguration() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the the startup configuration.
getConfiguration() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Get the configuration.
getConfPrefix() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor: Get the configuration prefix of the processor.
getConfPrefix() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
getConfPrefix() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
getContaminantGenomes() - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenGenomes: Get the collection of genomes contaminants can be used for mapping.
getContaminationThreshold() - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector: Gets the contamination threshold.
getContent() - Method in class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Get the content of the message.
getCountReadsMapped() - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult
getCountReadsProcessed() - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult
getCurrentPid() - Static method in class fr.ens.biologie.genomique.aozan.Common: Return the pid of the instance of jvm.
getData() - Method in class fr.ens.biologie.genomique.aozan.QCReport: Get the data.
getDataStorage() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider
getDataStorage() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider
getDataStorage() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider
getDataStorage() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProvider: Get the data storage of used by the provider.
getDemuxStepRecipe() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the demux step recipe.
getDemuxToolName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor: Get the demultiplexing tool name.
getDemuxToolName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
getDemuxToolName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
getDescription() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.action.Action: Get action description.
getDescription() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.DoradoAction
getDescription() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ExecAction
getDescription() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.GuppyAction
getDescription() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.LegacyAction
getDescription() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ListAction
getDescription() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.SampleSheetConvertAction
getDescription() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Get the recipe name
getDescription() - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSource: Get the description of the sequencer.
getDescription() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the description of the sample in run.
getDescription() - Method in interface fr.ens.biologie.genomique.aozan.tests.AozanTest: Get the description of the test.
getDescription() - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractGlobalTest
getDescription() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest
getDescription() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
getDescription() - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest
getDescription() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest
getDescriptiveStatistics() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Returns the instance of DescriptiveStatistics.
getDescriptiveStatisticsWithZero() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Returns the instance of DescriptiveStatistics which doesn't contain the value zero.
getDiskUsage() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Get the disk usage of the data location.
getDouble(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get a double configuration key.
getDouble(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a double key.
getDouble(String) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field as a double.
getDouble(String, double) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get a double value for a configuration key.
getDouble(String, double) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a setting value as a double value.
getDouble(String, double) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a double key.
getDouble(String, double) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field as a double.
getEmail() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor.ProcessResult: Get the output email
getEmail() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SimpleProcessResult
getEndRunStepRecipe() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the new run step recipe.
getErrorExitCode() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the exit code to use when an error occurs.
getExcludePatterns() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.Tar: Get the list of patterns to exclude.
getFastqDir() - Method in class fr.ens.biologie.genomique.aozan.QC: Get the FASTQ directory of the run.
getFastqDirectory() - Method in class fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput: Get the bcl2fastq output directory of the run.
getFastqFilenames() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get list of fastq file names for this sample.
getFastqFiles() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get list of fastq files for this sample.
getFastqSampleParentDir() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Find fastq parent directory.
getFastqSamples() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Get the FASTQ samples.
getFastqScreenGenomes() - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreen
getFastqScreenResult() - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenPseudoMapReduce: Compile data of fastqscreen in percentage.
getFile(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a setting value as a File object.
getFilenamePrefix() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the prefix of the FASTQ file.
getFilenamePrefix(int) - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the prefix of the FASTQ file.
getFloat(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a float key.
getFloat(String) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field as a float.
getFloat(String, float) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a float key.
getFloat(String, float) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field as a float.
getFlowcellId() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the flowcell id.
getFlowCellId() - Method in class fr.ens.biologie.genomique.aozan.aozan3.IlluminaRunIdWrapper: Get the flow cell identifier.
getFormat() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Get the format of the data.
getFullVersion() - Method in class fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput: Get the full bcl2fastq version used to generate the FASTQ files.
getGenericLogger() - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger
getGenomeDescStorage() - Method in class fr.ens.biologie.genomique.aozan.Storages: Get the genome description storage.
getGenomeIndexStorage() - Method in class fr.ens.biologie.genomique.aozan.Storages: Get the genome index storage.
getGenomeStorage() - Method in class fr.ens.biologie.genomique.aozan.Storages: Get the genome storage.
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractFastQCSampleTest: Get the anchor index of for the module in FastQC HTML report.
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCAdapterContentSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCBasicStatsSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCDuplicationLevelSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCKmerContentSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCNContentSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCOverrepresentedSequencesSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerBaseQualityScoresSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerBaseSequenceContentSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerSequenceGCContentSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerSequenceQualityScoresSampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerTileSequenceQualitySampleTest
getHTMLAnchorIndex() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCSequenceLengthDistributionSampleTest
getId() - Method in class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Get the id of the message.
getId() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunId: Get the id of the run.
getId() - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSource: Get the identifier of the sequencer.
getIlluminaSequencerName(RunId) - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerNames: Get the name of an Illumina sequencer from a runId.
getIncludePatterns() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.Tar: Get the list of patterns to include.
getIndex() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Gets the index.
getIndexedReadCount() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the indexed read count in run.
getIndexSample(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the sequence index related to a sample.
getInputRequirements() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor
getInputRequirements() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2QCDataProcessor
getInputRequirements() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor: Get the input requirements of the processor.
getInputRequirements() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DiscoverNewIlluminaRunDataProcessor
getInputRequirements() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor
getInputRequirements() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.EndIlluminaRunDataProcessor
getInputRequirements() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.GuppyONTBasecallingDataProcessor
getInputRequirements() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.IlluminaSyncDataProcessor
getInputRequirements() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Step: Get the input requirements of the processor.
getInstance() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.action.ActionService: Retrieve the singleton static instance of an DataProcessorService.
getInstance() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessorService: Retrieve the singleton static instance of an DataProcessorService.
getInstance() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProviderService: Retrieve the singleton static instance of an RunConfigurationProviderService.
getInstance() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the instance of the Main class.
getInstance() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.RunConfigurationProviderService: Retrieve the singleton static instance of an RunConfigurationProviderService.
getInstance() - Static method in class fr.ens.biologie.genomique.aozan.fastqc.OverrepresentedSequencesBlast: Get the singleton instance.
getInstance() - Static method in class fr.ens.biologie.genomique.aozan.fastqscreen.GenomeAliases: Create a instance of GenomeAliases or if it exists return instance.
getInstance() - Static method in class fr.ens.biologie.genomique.aozan.Storages: Get the instance of the singleton.
getInstrumentSerialNumber() - Method in class fr.ens.biologie.genomique.aozan.aozan3.IlluminaRunIdWrapper: Get the instrument serial number.
getInt(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get an int configuration key.
getInt(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get an integer key.
getInt(String) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field as an int.
getInt(String, int) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get an integer value for a configuration key.
getInt(String, int) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a setting value as an integer value.
getInt(String, int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get an integer key.
getInt(String, int) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field as an integer.
getInterval() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest
getJavaExecutablePath() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get java executable path.
getJVMArgs() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get JVM arguments.
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractSimpleGlobalTest: Get the the key in the RunData object for the value to test.
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.BaseCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.CycleCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.LaneCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.LoadingConcentrationPercentGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanPFClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanPhiXRawClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanRawClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianPFClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianPhiXRawClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianRawClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.NonIndexedBaseCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterPercentGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterSDGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXAlignPercentGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterSDGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.RawClusterCountGlobalTest
getKey() - Method in class fr.ens.biologie.genomique.aozan.tests.global.RawClusterSDGlobalTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest: Get the the key in the RunData object for the value to test.
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.GenomeNamesPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.IsIndexedPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.LaneCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MaxPFClusterCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MaxRawClusterCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MinPFClusterCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MinRawClusterCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFClusterCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFClusterRecoveryCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RawClusterCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RawClusterRecoveryCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.SampleCountPooledSampleTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest: Get the the key in the RunData object for the value to test.
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.FastQScreenSampleOvercontaminationCountProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.GenomeNamesProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.IsIndexedProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.LaneCountProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.MaxPFClusterCountProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.MaxRawClusterCountProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.MinPFClusterCountProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.MinRawClusterCountProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.PFClusterCountProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.RawClusterCountProjectTest
getKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.SampleCountProjectTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest: Get the the key in the RunData object for the value to test.
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityPFLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle100ErrorRateLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle20IntensityPercentLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle35ErrorRateLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle75ErrorRateLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.DensityLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ErrorRateLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.FirstCycleIntensityLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.OccupancyPercentLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterCountLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.RawClusterCountLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldLaneTest
getKey(int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldPFLaneTest
getKey(int, int, int, int, boolean) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest: Get the the key in the RunData object for the value to test.
getKey(int, int, int, int, boolean) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedExceptRefGenomeSampleTest
getKey(int, int, int, int, boolean) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest
getKey(int, int, int, int, boolean) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.GenomeNamesSampleTest
getKey(int, int, int, int, boolean) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.PFClusterCountSampleTest
getKey(int, int, int, int, boolean) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RawClusterCountSampleTest
getKey(int, int, int, int, boolean) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverablePFClusterCountSampleTest
getKey(int, int, int, int, boolean) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverableRawClusterCountSampleTest
getKeyMap(int, int) - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.ErrorMetricsCollector: Set unique id for each pair lane-read in a run.
getLane() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the number of lane from the sample in run.
getLaneCount() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the lane count in run.
getLanePFClusterRecoveryCount(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the passing filter cluster recovery count for a lane.
getLaneRawClusterRecoveryCount(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the raw cluster recovery count for a lane.
getLastRunData() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData
getLocation() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Get the location of the data.
getLockDirectory(Recipe) - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the path where creating locks of a recipe.
getLogger() - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Get the logger object.
getLogger() - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Get the underlying logger.
getLogger() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Get the logger.
getLogger() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Get the logger.
getLoggerName() - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Get the logger name.
getLong(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get a long configuration key.
getLong(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a long key.
getLong(String) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field as a long.
getLong(String, int) - Method in class fr.ens.biologie.genomique.aozan.util.CSVLineParser: Get the value of a field as a long.
getLong(String, long) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get a long value for a configuration key.
getLong(String, long) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a long key.
getLongArray(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get an longTable key.
getLongArray(String, long[]) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get a long array key.
getMachine() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Get the machine of the storage
getMainLockPath() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the main lock path.
getManufacturer() - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSource: Get the manufacturer of the sequencer.
getMap() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the map.
getMax() - Method in class fr.ens.biologie.genomique.aozan.util.DoubleInterval: Get the maximal value of the interval.
getMax() - Method in class fr.ens.biologie.genomique.aozan.util.LongInterval: Get the maximal value of the interval.
getMax() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils
getMean() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the mean for values.
getMeanToInteger() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the mean for values.
getMeanWithoutZero() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the mean for values which are different of 0.
getMeanWithoutZeroToInteger() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the mean for values which are different of 0
getMediane() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the median for values.
getMedianeToInteger() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the median for values.
getMedianWithoutZero() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the median for values which are different of 0.
getMedianWithoutZeroToInteger() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the median for values which are different of 0.
getMessage() - Method in class fr.ens.biologie.genomique.aozan.tests.TestResult: Get the message of the result.
getMethodName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ActionService
getMethodName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessorService
getMethodName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProviderService
getMethodName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.RunConfigurationProviderService
getMin() - Method in class fr.ens.biologie.genomique.aozan.util.DoubleInterval: Get the minimal value of the interval.
getMin() - Method in class fr.ens.biologie.genomique.aozan.util.LongInterval: Get the minimal value of the interval.
getMin() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils
getModel() - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSource: Get the model of the sequencer.
getName() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.action.Action: Get the name of the action.
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.DoradoAction
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ExecAction
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.GuppyAction
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.LegacyAction
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ListAction
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.SampleSheetConvertAction
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2QCDataProcessor
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
getName() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor: Get the name of the processor.
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DiscoverNewIlluminaRunDataProcessor
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.EndIlluminaRunDataProcessor
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.GuppyONTBasecallingDataProcessor
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.IlluminaSyncDataProcessor
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider
getName() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProvider: Get the name of the provider.
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Get the recipe name
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Step: Get the name of the step.
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.EmptyRunConfigurationProvider
getName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.IlluminaSamplesheetRunConfigurationProvider
getName() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.RunConfigurationProvider: Get the name of the run configuration provider.
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.AozanCollector
getName() - Method in interface fr.ens.biologie.genomique.aozan.collectors.Collector: Get the name of the collector.
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.FastQCCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.ErrorMetricsCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.ExtractionMetricsCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.interop.TileMetricsCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.ReadCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector: Get collector name.
getName() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
getName() - Method in interface fr.ens.biologie.genomique.aozan.tests.AozanTest: Get the name of the test.
getName() - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractGlobalTest
getName() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest
getName() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
getName() - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest
getName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest
getNameFromSerialNumber(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerNames: Get the name of a sequencer from its serial number.
getNameGenome() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest: Get name of reference genome.
getNameGenome() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest: Get name of reference genome.
getNewRunStepRecipe() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the new run step recipe.
getNormalizedSampleGenome(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the normalized sample genome.
getOriginalRunId() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunId: Get the id of the run.
getPath() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Get the path of the data.
getPath() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Get the path of the storage.
getPath(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get Path configuration key.
getPath(String, Path) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Get a Path value for a configuration key.
getPercentMappedReadOnContaminationSample(int, int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the percent mapped read on dataset contaminants.
getPooledSampleCount() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the pooled sample count.
getPooledSampleDemuxName(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the demultiplexing name of a pooled sample.
getPooledSampleDescription(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the description of a pooled sample.
getPooledSampleIndex(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the index of a pooled sample.
getPooledSampleProject(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the project id of a pooled sample.
getPooledSampleProjectName(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the project name of a pooled sample.
getPooledSamples() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get all samples ids (without undetermined samples) of the run.
getPoreType(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Get the pore type from the flowcell reference
getProcessorName() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Step: Get the name of the processor of the step.
getProjectCount() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the project count.
getProjectId(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the id of a project from its name.
getProjectName() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the project name from the sample in run.
getProjectName(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the name of a project.
getProjects() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get all project identifiers of the run.
getProjectSample(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the project related to a sample.
getQcDir() - Method in class fr.ens.biologie.genomique.aozan.QC: Get the QC directory of the run.
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractFastQCSampleTest: Get the name of the FastQC module.
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCAdapterContentSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCBasicStatsSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCDuplicationLevelSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCKmerContentSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCNContentSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCOverrepresentedSequencesSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerBaseQualityScoresSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerBaseSequenceContentSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerSequenceGCContentSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerSequenceQualityScoresSampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCPerTileSequenceQualitySampleTest
getQCModuleName() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQCSequenceLengthDistributionSampleTest
getQCStepRecipe() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the QC step recipe.
getRead() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the number of read from the sample in run.
getReadCount() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the read count in run.
getReadCyclesCount(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the cycles count in the read.
getReadPFClusterCount(int, int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the passing filter cluster count related to a lane and a read.
getReadPrcAlign(int, int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the percent align Phix related to the lane and the read.
getReadRawClusterCount(int, int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the raw cluster count related to a lane and a read.
getReadsprocessed() - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenSAMParser
getRecipeDoneDenyFilename(Recipe) - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the done filename for a recipe.
getRecipeName(Path) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder: Load a file and try to get the recipe name inside if it is a recipe file.
getRecipePath(List<RecipeFinder.RecipePath>, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder: Get the path of a recipe in a list of recipes.
getRecipes() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder: Get the recipes existing in the directory.
getReportDirectory() - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector: Gets the report directory.
getResult(String) - Method in class fr.ens.biologie.genomique.aozan.fastqc.OverrepresentedSequencesBlast: Get the blast result of a sequence
getRunConfiguration(RunData) - Method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.EmptyRunConfigurationProvider
getRunConfiguration(RunData) - Method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.IlluminaSamplesheetRunConfigurationProvider
getRunConfiguration(RunData) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.RunConfigurationProvider: Get the run configuration for a run data
getRunData() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor.ProcessResult: Get the output data.
getRunData() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SimpleProcessResult
getRundataPrefix() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Create the prefix used for add data in a RunData for each FastqSample.
getRunId() - Method in class fr.ens.biologie.genomique.aozan.aozan3.IlluminaRunIdWrapper: Get RunId.
getRunId() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Get run Id.
getRunId() - Method in class fr.ens.biologie.genomique.aozan.QC: Get the run id.
getRunMode() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the run mode.
getRunNumber() - Method in class fr.ens.biologie.genomique.aozan.aozan3.IlluminaRunIdWrapper: Get the run number.
getRunTilesPerLane() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the run tiles per lane.
getSampleCount() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the sample count.
getSampleDemuxName(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the demultiplexing name of a sample.
getSampleDescription(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the description of a sample.
getSampleDirectoryName() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the directory name of the sample.
getSampleGenome(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the sample genome.
getSampleGenomes() - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenGenomes: Get the collection genomes name can be used for the mapping.
getSampleId() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the sample Id.
getSampleId(int, String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the identifier of sample from its lane and demuxmultiplexing name.
getSampleIdentifier(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the sample identifier string.
getSampleIndex(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the index of a sample.
getSampleIndex2(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the index of a sample.
getSampleKey(int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest: Get the the key in the RunData object for the value to test.
getSampleLane(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the lane of a sample.
getSampleName() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the sample name in run.
getSampleName(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the name of a sample.
getSamplePFClusterCount(int, int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the passing filter cluster count for a sample.
getSamplePFClusterRecoveryCount(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the passing filter cluster recovery count for a sample.
getSampleRawClusterCount(int, int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the raw cluster count for a sample.
getSampleRawClusterRecoveryCount(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the raw cluster recovery count for a sample.
getSamples() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get all samples identifiers (without undetermined samples) of the run.
getSampleSheet() - Method in class fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput: Get the sample sheet.
getSampleSheet() - Method in class fr.ens.biologie.genomique.aozan.QC: Get the samplesheet file.
getSampleSheet(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a sample sheet.
getSampleSheet(String) - Method in class fr.ens.biologie.genomique.aozan.tests.TestConfiguration: Get a sample sheet.
getSamplesInLane(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get all samples identifiers (without undetermined samples) related to the lane as a list.
getSamplesInPooledSample(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the list of sample identifiers in a pooled sample.
getSamplesInProject(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the list of the samples of a project.
getScore() - Method in class fr.ens.biologie.genomique.aozan.tests.TestResult: Get the score of the test
getScore(Number) - Method in class fr.ens.biologie.genomique.aozan.util.ScoreInterval
getSendMail() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Return SendMail object.
getSequencerApplicationName() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the sequencer application name.
getSequencerApplicationVersion() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the sequencer application version.
getSequencerFamily() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the sequencer family.
getSequencerName() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the sequencer name.
getSequencerRTAVersion() - Method in class fr.ens.biologie.genomique.aozan.RunData: Gets the RTA version.
getSequencerSource() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage
getSequencingTechnology() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Get the sequencing technology used for the data.
getSerialNumber() - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSource: Get the serial number of the sequencer.
getSettings() - Method in class fr.ens.biologie.genomique.aozan.QC: Get Aozan settings.
getSource() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Get the source of the data (e.g.
getStandardDeviation() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the standard deviation for values.
getStandardDeviation(boolean) - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the standard deviation for values.
getStandardDeviationToInteger() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the standard deviation for values.
getStorage() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Get the storage of the data location.
getStorages() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Get storages
getSubject() - Method in class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Get the subject of the message.
getSubmittedSequenceCount() - Method in class fr.ens.biologie.genomique.aozan.fastqc.OverrepresentedSequencesBlast: Get the number of submitted sequences
getSubsetFastqFile() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Return the temporary if exists which correspond to the key.
getSubsetFastqFilename() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Get the name for temporary fastq files uncompressed.
getSum() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the sum of values.
getSumToInteger() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Compute the sum of values.
getSyncStepRecipe() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the synchronization step recipe.
getTemporaryDir() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Get the temporary path.
getTheOnlyElement() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Get the only RunData element in the collection
getThreadsNumber() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Return the number of thread that the collector can be used for execution.
getThreadsNumber() - Method in class fr.ens.biologie.genomique.aozan.collectors.FastQCCollector
getThreadsNumber() - Method in class fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector: Get number of thread.
getThreadsNumber() - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector
getThreadsNumber() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
getTilesCount() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the tiles count.
getTmpDir() - Method in class fr.ens.biologie.genomique.aozan.QC: Get the temporary directory.
getToolVersion(RunId, String, List<String>, boolean, Function<List<String>, String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.ExternalTool: Get the tool executable version.
getTotalSpace() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Get the total space of the storage.
getTrimmedLowerCase(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration: Get a setting value in lower case.
getType() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Get the type of the data.
getType() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Get the type of the data.
getType() - Method in class fr.ens.biologie.genomique.aozan.tests.TestResult: Get the type of the result message.
getUnallocatedSpace() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Get the unallocated space of the storage.
getUncompressedSize() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Returns a estimation of the size of uncompressed fastq files according to the type extension of files and the coefficient of uncompression corresponding.
getUnit() - Method in interface fr.ens.biologie.genomique.aozan.tests.AozanTest: Get the unit of the result of the test.
getUnit() - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractGlobalTest
getUnit() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest
getUnit() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
getUnit() - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest
getUnit() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest
getUsableSpace() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Get the usable space of the storage.
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractSimpleGlobalTest: Get the type of the value.
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.BaseCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.CycleCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.LaneCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.LoadingConcentrationPercentGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanPFClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanPhiXRawClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanRawClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianPFClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianPhiXRawClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianRawClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.NonIndexedBaseCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterPercentGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterSDGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXAlignPercentGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterSDGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.RawClusterCountGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.global.RawClusterSDGlobalTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest: Get the type of the value.
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityPFLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle100ErrorRateLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle20IntensityPercentLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle35ErrorRateLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle75ErrorRateLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.DensityLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ErrorRateLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.FirstCycleIntensityLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.OccupancyPercentLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterCountLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.RawClusterCountLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldPFLaneTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest: Get the type of the value.
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.GenomeNamesPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.IsIndexedPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.LaneCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MaxPFClusterCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MaxRawClusterCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MinPFClusterCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.MinRawClusterCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFClusterCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFClusterRecoveryCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RawClusterCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RawClusterRecoveryCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.SampleCountPooledSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest: Get the type of the value.
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.FastQScreenSampleOvercontaminationCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.GenomeNamesProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.IsIndexedProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.LaneCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MaxPFClusterCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MaxRawClusterCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MinPFClusterCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.MinRawClusterCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.PFClusterCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.RawClusterCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.project.SampleCountProjectTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest: Get the type of the value.
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedExceptRefGenomeSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.GenomeNamesSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.PFClusterCountSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RawClusterCountSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverablePFClusterCountSampleTest
getValueType() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverableRawClusterCountSampleTest
getVarPath() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Get the path for var files.
getVersion() - Method in class fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput: Get the bcl2fastq version used to generate the FASTQ files.
Globals - Class in fr.ens.biologie.genomique.aozan.aozan3: This class contains Globals constants.
Globals - Class in fr.ens.biologie.genomique.aozan: This class contains Globals constants.
GlobalStatsCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This class define a Collector for global statistics of the run.
GlobalStatsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector
GlobalTest - Interface in fr.ens.biologie.genomique.aozan.tests.global: This interface define a test on lane.
GuppyAction - Class in fr.ens.biologie.genomique.aozan.aozan3.action: This class define an guppy action that will launch Guppy.
GuppyAction() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.action.GuppyAction
GuppyONTBasecallingDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class implements a Guppy data processor.
GuppyONTBasecallingDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.GuppyONTBasecallingDataProcessor
GZIP - fr.ens.biologie.genomique.aozan.aozan3.util.UnTar.Compression

H

hashCode() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType
hashCode() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunId
hashCode() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.EntityStat
help(Options) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Show command line help.
HISEQ_1000 - fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.IlluminaModel
HISEQ_1500 - fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.IlluminaModel
HISEQ_2000 - fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.IlluminaModel
HISEQ_2500 - fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.IlluminaModel
HISEQ_CRITICAL_MIN_SPACE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Hiseq critical minimum space.
HISEQ_DATA_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: hiseq directory data path.
HISEQ_SPACE_FACTOR_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Hiseq space factor.
HISEQ_STEP_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Hiseq step.
HISEQ_WARNING_MIN_SPACE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Hiseq warning minimum space.

I

ILLUMINA - fr.ens.biologie.genomique.aozan.aozan3.DataType.SequencingTechnology
ILLUMINA - fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.Manufacturer
ILLUMINA_FASTQ - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.DataType
IlluminaProcessedRunDataProvider - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprovider: This class define a processed data provider for Illumina runs.
IlluminaProcessedRunDataProvider() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider
IlluminaRawRunDataProvider - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprovider: This class define a processed data provider for Illumina runs.
IlluminaRawRunDataProvider() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider
IlluminaRunIdWrapper - Class in fr.ens.biologie.genomique.aozan.aozan3: This class allow to get information from Illumina run id.
IlluminaRunIdWrapper(RunId) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.IlluminaRunIdWrapper: Constructor.
IlluminaSampleSheetConverter - Class in fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter: This class define a converter between an Illumina samplesheet in XLS format to CSV.
IlluminaSampleSheetConverter(File, File) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.IlluminaSampleSheetConverter: Abstract constructor.
IlluminaSamplesheetRunConfigurationProvider - Class in fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider: Get the run configuration from an Illumina samplesheet.
IlluminaSamplesheetRunConfigurationProvider() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.IlluminaSamplesheetRunConfigurationProvider
IlluminaSyncDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define an Illumina synchronization data processor.
IlluminaSyncDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.IlluminaSyncDataProcessor
IlluminaUtils - Class in fr.ens.biologie.genomique.aozan.aozan3: This class contents some utility methods for Illumina.
INDEX_HTML_TEMPLATE_FILENAME - Static variable in class fr.ens.biologie.genomique.aozan.Globals
INDEX_HTML_TEMPLATE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Index html template path.
INDEX_SEQUENCES_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Index sequences path.
IndexGenerator - Class in fr.ens.biologie.genomique.aozan.aozan3.legacy: This class allow to generate index file like for Aozan 1.x and 2.x.
IndexGenerator() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.legacy.IndexGenerator
info(RunData, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an info message.
info(RunId, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an info message.
info(GenericLogger, RunData, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an info message.
info(GenericLogger, RunId, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an info message.
info(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log an info message.
init() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Initialize the steps of the recipe
init() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Step: Initialize the step.
init() - Method in interface fr.ens.biologie.genomique.aozan.tests.AozanTest: Initialize the test.
init() - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractGlobalTest
init() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractLaneTest
init() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractPooledSampleTest
init() - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractProjectTest
init() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSampleTest
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2QCDataProcessor
init(Configuration, GenericLogger) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor: Initialize the processor.
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DiscoverNewIlluminaRunDataProcessor
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.EndIlluminaRunDataProcessor
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.GuppyONTBasecallingDataProcessor
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SyncDataProcessor
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.EmptyRunConfigurationProvider
init(Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.IlluminaSamplesheetRunConfigurationProvider
init(Configuration, GenericLogger) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.RunConfigurationProvider: Initialize the run configurator provider.
init(DataStorage, Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider
init(DataStorage, Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider
init(DataStorage, Configuration, GenericLogger) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider
init(DataStorage, Configuration, GenericLogger) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProvider: Initialize the provider.
init(String, String, String, GenericLogger) - Static method in class fr.ens.biologie.genomique.aozan.Storages: Initialize the singleton.
initConsoleHandler() - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Initialize the console logger handler for Hadoop mappers and reducers.
initConsoleHandler(Level) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Initialize the console logger handler for Hadoop mappers and reducers.
initialize(Settings) - Static method in class fr.ens.biologie.genomique.aozan.fastqscreen.GenomeAliases: Create a instance of GenomeAliases or if it exists return instance.
initLogger(String) - Static method in class fr.ens.biologie.genomique.aozan.Common: Initialize the logger for the application.
initLogger(String, String) - Static method in class fr.ens.biologie.genomique.aozan.Common: Initialize the logger for the application.
initLogger(String, Level) - Static method in class fr.ens.biologie.genomique.aozan.Common: Initialize the logger for the application.
InLanePercentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a sample percent in lane test.
InLanePercentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.InLanePercentSampleTest: Public constructor.
InProjectPercentPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define test to compute the percent reads passing filter on all samples replica in run.
InProjectPercentPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.InProjectPercentPooledSampleTest: Public constructor.
InputData - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define InputData for processors.
InputData() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: This constructor create an empty InputData.
InputData(RunData) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Create a new object with one element
InputData(Collection<RunData>) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Create a new object with the content of a collection of RunData objects.
inputFile - Variable in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter
InRunPercentPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define test to compute the percent reads passing filter on all samples replica in run.
InRunPercentPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.InRunPercentPooledSampleTest: Public constructor.
INTEROP - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.DataType
Interval - Interface in fr.ens.biologie.genomique.aozan.util: This interface define an interval.
isAozanEnabled() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Test if Aozan is enabled.
isCollectorEnabled(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Test if a collector is enabled.
isCompressLogs() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Test if log compression is enabled.
isCompressSequencingSummary() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Test if log sequencing summary file compression is enabled.
isCompressSequencingTelemetry() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Test if log telemetry file compression is enabled.
isDirectory() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Test if the data location is a directory.
isEmpty() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Test if the configuration is empty.
isEmpty() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Test if the collection is empty.
isEmpty() - Method in class fr.ens.biologie.genomique.aozan.tests.TestConfiguration: Test if the configuration is empty.
isEnoughSpace(long) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Test if there is enough space on the storage for a required amount of disk space.
isErrorMessage() - Method in class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Test if the message is an error message.
isFastqMergin() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Test if FASTQ merging is enabled.
isFile() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Test if the data location is a regular file.
isGenomeDescStorage() - Method in class fr.ens.biologie.genomique.aozan.Storages: Test if a genome description storage exists.
isGenomeIndexStorage() - Method in class fr.ens.biologie.genomique.aozan.Storages: Test if a genome index storage exists.
isGenomeStorage() - Method in class fr.ens.biologie.genomique.aozan.Storages: Test if a genome storage exists.
isHidden() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.action.Action: Test if the action must be hidden from the list of available actions.
isHidden() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.DoradoAction
isHidden() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ExecAction
isHidden() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.GuppyAction
isHidden() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.LegacyAction
isHidden() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.ListAction
isHidden() - Method in class fr.ens.biologie.genomique.aozan.aozan3.action.SampleSheetConvertAction
IsIndexedPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The Class IsIndexedProjectTest.
IsIndexedPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.IsIndexedPooledSampleTest: Public constructor.
IsIndexedProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The Class IsIndexedProjectTest.
IsIndexedProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.IsIndexedProjectTest: Public constructor.
isIndexedSample(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Test if the sample is an indexed sample.
isInInterval(Number) - Method in class fr.ens.biologie.genomique.aozan.util.DoubleInterval
isInInterval(Number) - Method in interface fr.ens.biologie.genomique.aozan.util.Interval: Test if a number is in an interval.
isInInterval(Number) - Method in class fr.ens.biologie.genomique.aozan.util.LongInterval
isInstance() - Static method in class fr.ens.biologie.genomique.aozan.Storages: Test if the instance of the singleton has been initialized.
isLaneControl(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Check if the lane related to the sample name is a control lane.
isLaneIndexed(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Checks if is lane indexed.
isLocked() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.AozanLock: Check if lock is locked.
isLogMerging() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Test if logs merging is enabled.
isLogOnly() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Test if the run data is partial.
isMaxIncluded() - Method in class fr.ens.biologie.genomique.aozan.util.DoubleInterval: Test if the maximal value is included in the interval.
isMaxIncluded() - Method in class fr.ens.biologie.genomique.aozan.util.LongInterval: Test if the maximal value is included in the interval.
isMinIncluded() - Method in class fr.ens.biologie.genomique.aozan.util.DoubleInterval: Test if the minimal value is included in the interval.
isMinIncluded() - Method in class fr.ens.biologie.genomique.aozan.util.LongInterval: Test if the minimal value is included in the interval.
isNoMessage() - Method in class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Test if the message must be sent.
isOneElement() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Test if the size of the collection is 1.
isOriginalId() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunId: Test if the run Id is the original run Id.
isOutputMustExists() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor: Test if output directory must exists before launching demultiplexing.
isOutputMustExists() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
isOutputMustExists() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
isPartialData() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Test if the run data is partial.
isProcessAllReads() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Test if all reads (e.g.
isProcessAllReads() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
isProcessStandardSamples() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Test if standard samples must be processed.
isProcessStandardSamples() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
isProcessUndeterminedIndicesSamples() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Test if undetermined indices samples must be processed.
isProcessUndeterminedIndicesSamples() - Method in class fr.ens.biologie.genomique.aozan.collectors.FastQCCollector
isProcessUndeterminedIndicesSamples() - Method in class fr.ens.biologie.genomique.aozan.collectors.FastqScreenCollector
isProcessUndeterminedIndicesSamples() - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector
isProcessUndeterminedIndicesSamples() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
isProjectStatisticsCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector: Checks if is project statistics collector.
isProjectStatisticsCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector
isProjectStatisticsCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector
isReadable() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Test if the data location is readable.
isReadIndexed(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Check if the read is indexed.
isRecipe(List<RecipeFinder.RecipePath>, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder: Test if a recipe exists in a list of recipes.
isRecipeUnique(List<RecipeFinder.RecipePath>, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder: Test if a recipe is unique in a list of recipes.
isSampleStatisticsCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector: Checks if is sample statistics collector.
isSampleStatisticsCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector
isSampleStatisticsCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.AozanCollector
isSummaryCollector() - Method in interface fr.ens.biologie.genomique.aozan.collectors.Collector: Test if the class is a summary collector.
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.GlobalStatsCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.ReadCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector
isSummaryCollector() - Method in class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector
isUncompressedNeeded() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Return if it must uncompress fastq files else false.
isUndeterminedIndex() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample: Test if the sample is an undetermined index sample.
isUndeterminedInLane(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Check if undetermined FASTQ file exist for a lane.
isUndeterminedPooledSample(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Test if the sample is an undetermined sample.
isUndeterminedSample(int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Test if the sample is an undetermined sample.
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractSimpleGlobalTest: Test if the value is a percent.
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterPercentGlobalTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXAlignPercentGlobalTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest: Test if the value is a percent.
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle100ErrorRateLaneTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle20IntensityPercentLaneTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle35ErrorRateLaneTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle75ErrorRateLaneTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ErrorRateLaneTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest: Test if the value is a percent.
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest: Test if the value is a percent.
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest: Test if the value is a percent.
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedExceptRefGenomeSampleTest
isValuePercent() - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest
isWritable() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Returns if the storage is writable.
isWriteable() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation: Test if the data location is writable.
iterator() - Method in class fr.ens.biologie.genomique.aozan.util.CVSParser

J

JSONUtils - Class in fr.ens.biologie.genomique.aozan.aozan3.util: This class contains some utility methods for JSON serialization.

L

LANE_COUNT - Static variable in class fr.ens.biologie.genomique.aozan.QC
LaneCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a lane count global test.
LaneCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.LaneCountGlobalTest: Public constructor.
LaneCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The Class LanesRunProjectTest.
LaneCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.LaneCountPooledSampleTest: Public constructor.
LaneCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The Class LanesRunProjectTest.
LaneCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.LaneCountProjectTest: Public constructor.
LaneTest - Interface in fr.ens.biologie.genomique.aozan.tests.lane: This interface define a test on lane.
LegacyAction - Class in fr.ens.biologie.genomique.aozan.aozan3.action: This class define an legacy action.
LegacyAction() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.action.LegacyAction
LegacyRecipes - Class in fr.ens.biologie.genomique.aozan.aozan3.legacy: This class define recipes that perform like Aozan 2 steps.
LegacyRecipes(Configuration, GenericLogger, Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes
LICENSE_TXT - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: Licence text.
LICENSE_TXT - Static variable in class fr.ens.biologie.genomique.aozan.Globals: Licence text.
ListAction - Class in fr.ens.biologie.genomique.aozan.aozan3.action: This class define an action that list existing recipes.
ListAction() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.action.ListAction
listCompletedRunData() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProvider: List available completed runs.
listCompletedRunData(Collection<RunId>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider
listCompletedRunData(Collection<RunId>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider
listCompletedRunData(Collection<RunId>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider
listCompletedRunData(Collection<RunId>) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProvider: List available runs in progress.
listInProgressRunData() - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProvider: List available runs in progress.
listInProgressRunData(Collection<RunId>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider
listInProgressRunData(Collection<RunId>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider
listInProgressRunData(Collection<RunId>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider
listInProgressRunData(Collection<RunId>) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProvider: List available runs in progress.
load() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.RunIdStorage: Load run ids.
load(Path) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Load configuration.
load(Path, boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Load configuration.
LoadingConcentrationPercentGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a loading concentration percent global test.
LoadingConcentrationPercentGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.LoadingConcentrationPercentGlobalTest
loadSampleSheet() - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter: Load the samplesheet.
loadSampleSheet() - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.IlluminaSampleSheetConverter
loadSampleSheet() - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.NanoporeSampleSheetConverter
LOCK_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Lock file.
LOG_FORMATTER - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Format of the log.
LOG_FORMATTER - Static variable in class fr.ens.biologie.genomique.aozan.Globals: Format of the log.
LOG_LEVEL - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The log level of the application.
logAozanStart() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Log the start of the application.
logAozanStop() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.LegacyRecipes: Log the end of the application.
logConfig(String) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Log a CONFIG message using getLogger().config().
logFiner(String) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Log a FINER message using getLogger().finer().
logFinest(String) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Log a FINEST message using getLogger().finest().
logInfo(String) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Log an INFO message using getLogger().info().
logSevere(String) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Log an SEVERE message using getLogger().severe().
logThreadEnd(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqThread
logThreadEnd(String) - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesProcessThread
logThreadStart() - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqThread
logThreadStart() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesProcessThread
logWarning(String) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Log an WARNING message using getLogger().warning().
LongInterval - Class in fr.ens.biologie.genomique.aozan.util: This class define a long interval.
LongInterval(long, boolean, long, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.util.LongInterval
LongInterval(long, long) - Constructor for class fr.ens.biologie.genomique.aozan.util.LongInterval
LongInterval(String) - Constructor for class fr.ens.biologie.genomique.aozan.util.LongInterval

M

MAIL_ERROR_TO_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Mail error to.
MAIL_FOOTER_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Mail footer.
MAIL_FROM_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Mail from.
MAIL_HEADER_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Mail header.
MAIL_TO_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Mail to.
main(String[]) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Main method of the program.
main(String[]) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.NanoporeSampleSheetConverter
main(String[]) - Static method in class fr.ens.biologie.genomique.aozan.demux.ReDemux
Main - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define the main class.
makeContaminantList() - Static method in class fr.ens.biologie.genomique.aozan.fastqc.ContaminantFinder
makeOptions() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Main: Create options for command line
map(String, List<String>, Reporter) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenPseudoMapReduce: Mapper Receive value in SAM format, only the read mapped are added in output with reference genome.
MathUtils - Class in fr.ens.biologie.genomique.aozan.util: This class contains useful math methods.
MaxPFClusterCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test the maximum on passing filter clusters on samples in a project.
MaxPFClusterCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.MaxPFClusterCountPooledSampleTest: Public constructor.
MaxPFClusterCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define a test the maximum on passing filter clusters on samples in a project.
MaxPFClusterCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.MaxPFClusterCountProjectTest: Public constructor.
MaxRawClusterCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test the maximum on raw clusters on samples in a project.
MaxRawClusterCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.MaxRawClusterCountPooledSampleTest: Public constructor.
MaxRawClusterCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define a test the maximum on raw clusters on samples in a project.
MaxRawClusterCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.MaxRawClusterCountProjectTest: Public constructor.
MeanPFClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster mean global test.
MeanPFClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.MeanPFClusterCountGlobalTest: Public constructor.
MeanPhiXRawClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster phix mean global test.
MeanPhiXRawClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.MeanPhiXRawClusterCountGlobalTest: Public constructor.
MeanRawClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster global test.
MeanRawClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.MeanRawClusterCountGlobalTest: Public constructor.
MedianPFClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster mediane global test.
MedianPFClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.MedianPFClusterCountGlobalTest: Public constructor.
MedianPhiXRawClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster phix mediane global test.
MedianPhiXRawClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.MedianPhiXRawClusterCountGlobalTest: Public constructor.
MedianRawClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster mediane global test.
MedianRawClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.MedianRawClusterCountGlobalTest: Public constructor.
MINIMAL_JAVA_VERSION_REQUIRED - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: Minimal java version required by Aozan.
MinPFClusterCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test the minimum on passing filter clusters on samples in a project.
MinPFClusterCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.MinPFClusterCountPooledSampleTest: Public constructor.
MinPFClusterCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define a test the minimum on passing filter clusters on samples in a project.
MinPFClusterCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.MinPFClusterCountProjectTest: Public constructor.
MinRawClusterCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test the minimum on raw clusters on samples in a project.
MinRawClusterCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.MinRawClusterCountPooledSampleTest: Public constructor.
MinRawClusterCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define a test the minimum on raw clusters on samples in a project.
MinRawClusterCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.MinRawClusterCountProjectTest: Public constructor.
mismatches(String, String) - Static method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesProcessThread: Get the number of mismatches of two string of the same length.
MultiDataTypeFilter - Class in fr.ens.biologie.genomique.aozan.aozan3.datatypefilter: This class define a filter that combine several other filters.
MultiDataTypeFilter(DataTypeFilter...) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.MultiDataTypeFilter: Constructor.
MULTIQC_DATA_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector
MultiQCCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This class define a MultiQC collector.
MultiQCCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.MultiQCCollector
MultiQCReportProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: This class define a test that allow access to the MultiQC report of a project.
MultiQCReportProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.MultiQCReportProjectTest: Public constructor.

N

names() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.DataStorageRegistry: Get the names of registered storages.
NANOPORE - fr.ens.biologie.genomique.aozan.aozan3.DataType.SequencingTechnology
NanoporeSampleSheetConverter - Class in fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter: This class define a converter between a Nanopore samplesheet in XLS format to CSV.
NanoporeSampleSheetConverter(File, File) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.NanoporeSampleSheetConverter: Abstract constructor.
newAozanLogger(GenericLogger) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Create an Aozan 3 Logger from a GenericLogger object.
newCategory(DataType.Category) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Create a new RunType object from the current object with a new type.
newCategory(DataType.Category) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Create a new RunType object from the current object with a new category.
newDataLocation(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Create a data location.
newDummyLogger() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Create dummy logger.
newGson() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.util.JSONUtils: Create a new Gson object with all required adapters for serialization of Aozan objects.
newIlluminaSequencerSource(RunId) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory: Create a new sequencer source from an Illumina runId.
newIlluminaSequencerSource(SequencerSourceFactory.IlluminaModel) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory: Create a new Illumina sequencer source.
newIlluminaSequencerSource(String, SequencerSourceFactory.IlluminaModel, String, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory: Create a new Illumina sequencer source.
newInstance(TestConfiguration) - Static method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenGenomes: Private constructor of FastqScreenGenomeMapper.
newLocation(DataLocation) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Create a new RunData object from the current object with a new location.
newLogger(Configuration, GenericLogger) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.AozanLoggerFactory: Configure logger.
newPartialProcessedIlluminaRunData(DataStorage, Path, SequencerSource) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.RunDataFactory: Create a new Illumina partial processed run data.
newPartialRawIlluminaRunData(DataStorage, Path, SequencerSource) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.RunDataFactory: Create a new partial Illumina run data.
newProcessedIlluminaRunData(DataStorage, Path, SequencerSource) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.RunDataFactory: Create a new Illumina processed run data.
newRawIlluminaRunData(DataStorage, Path, SequencerSource) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.RunDataFactory: Create a new Illumina run data.
newRunId(RunId) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Create a new RunData object from the current object with a new run Id.
newRunId(RunId, Map<String, String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DefaultRunIdGenerator
newRunId(RunId, Map<String, String>) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.RunIdGenerator: Create a new run id for the output of a processor.
newSimpleProcess(RunId, boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.ExternalTool: Create a new process.
newTechnology(DataType.SequencingTechnology) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Create a new RunType object from the current object with a new type.
newTechnology(DataType.SequencingTechnology) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Create a new RunType object from the current object with a new technology.
newType(DataType) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Create a new RunData object from the current object with a new type.
newType(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Create a new RunType object from the current object with a new type.
newType(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Create a new RunType object from the current object with a new type.
NEXTSEQ_500 - fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.IlluminaModel
noMessage() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.EmailMessage: Create a email without message that will be sent.
NONE - fr.ens.biologie.genomique.aozan.aozan3.util.UnTar.Compression
NonIndexedBaseCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a non indexed base count global test.
NonIndexedBaseCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.NonIndexedBaseCountGlobalTest: Public constructor.
nullToUnknownSource(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.ParserUtils: Return an unknown source string if the argument is null.

O

OccupancyPercentGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define an occupancy percent global test.
OccupancyPercentGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.OccupancyPercentGlobalTest: Public constructor.
OccupancyPercentLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define an occupancy percent lane test.
OccupancyPercentLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.OccupancyPercentLaneTest: Public constructor.
OTHER - fr.ens.biologie.genomique.aozan.aozan3.DataType.Category
outputDir - Variable in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter
outputFile - Variable in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter
OverrepresentedSequencesBlast - Class in fr.ens.biologie.genomique.aozan.fastqc: This class launches blastn on one sequence query and parses xml result file to identify the best hit.

P

PARAMETER_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The prefix of the parameters of the application.
PARAMETER_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The prefix of the parameters of the application.
parse(String) - Method in class fr.ens.biologie.genomique.aozan.util.CVSParser: Parse a line.
parse(NodeList, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.ConfigurationXMLParser
parse(NodeList, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeXMLParser
parse(NodeList, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.StepsXMLParser
parse(NodeList, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.StoragesXMLParser
parseAndSet(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Parse a string (e.g.
parseDemuxToolVersion(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor: Parse demultiplexing tool version.
parseDemuxToolVersion(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
parseDemuxToolVersion(List<String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
parseLines(InputStream) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenSAMParser: Parse a SAM file and create a new file mapoutsamfile, it contains a line for each read mapped with her name and mapping data : first character represent the number of hits for a read : 1 or 2 (for several hits) and the end represent the name of reference genome.
ParserUtils - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class contains Utility methods to parse XML documents.
parseVersion(String) - Static method in enum fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput.Bcl2FastqVersion
PARTIAL_BCL - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.DataType
PARTIAL_ILLUMINA_FASTQ - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.DataType
PARTIAL_INTEROP - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.DataType
PartialDataTypeFilter - Class in fr.ens.biologie.genomique.aozan.aozan3.datatypefilter: This class define a DataTypeFilter that require partial or not DataType.
PartialDataTypeFilter(boolean) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.PartialDataTypeFilter: Consctructor.
partialSync(Path, Path) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.IlluminaSyncDataProcessor
partialSync(Path, Path) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SyncDataProcessor
PFBaseMeanQualityScorePooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define test to compute the percent reads passing filter on all samples replica in run.
PFBaseMeanQualityScorePooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFBaseMeanQualityScorePooledSampleTest: Public constructor.
PFClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a Passing Filter cluster global test.
PFClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.PFClusterCountGlobalTest: Public constructor.
PFClusterCountLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a Passing Filter cluster lane test.
PFClusterCountLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterCountLaneTest: Public constructor.
PFClusterCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test the sum on passing filter clusters on samples in a project.
PFClusterCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFClusterCountPooledSampleTest: Public constructor.
PFClusterCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define a test the sum on passing filter clusters on samples in a project.
PFClusterCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.PFClusterCountProjectTest: Public constructor.
PFClusterCountSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a passing filter clusters count test for samples.
PFClusterCountSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.PFClusterCountSampleTest: Public constructor.
PFClusterPercentGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a percent passing filter clusters global test.
PFClusterPercentGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.PFClusterPercentGlobalTest: Public constructor.
PFClusterPercentLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class a test on passing filter cluster in a lane.
PFClusterPercentLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterPercentLaneTest: Public constructor.
PFClusterRecoveryCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test the maximum on raw clusters on samples in a project.
PFClusterRecoveryCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFClusterRecoveryCountPooledSampleTest: Public constructor.
PFClusterSDGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster standard deviation global test.
PFClusterSDGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.PFClusterSDGlobalTest: Public constructor.
PFPercentPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define test to compute the percent reads passing filter on all samples replica in run.
PFPercentPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFPercentPooledSampleTest: Public constructor.
PFPercentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a percent passing filter sample test.
PFPercentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.PFPercentSampleTest: Public constructor.
PhasingPrephasingPercentLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a lane test on phasing / prephasing.
PhasingPrephasingPercentLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.PhasingPrephasingPercentLaneTest
PhiXAlignPercentGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a lane test on PhiX percent aligned.
PhiXAlignPercentGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.PhiXAlignPercentGlobalTest: Public constructor.
PhiXAlignPercentLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a lane test on PhiX percent aligned.
PhiXAlignPercentLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.PhiXAlignPercentLaneTest: Public constructor.
PhiXRawClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster phix count global test.
PhiXRawClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterCountGlobalTest: Public constructor.
PhiXRawClusterCountLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a lane test on PhiX raw cluster count.
PhiXRawClusterCountLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.PhiXRawClusterCountLaneTest: Public constructor.
PhiXRawClusterSDGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster phix standard deviation global test.
PhiXRawClusterSDGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterSDGlobalTest: Public constructor.
PooledSampleComparator(RunData) - Constructor for class fr.ens.biologie.genomique.aozan.RunData.PooledSampleComparator: Constructor.
PooledSampleTest - Interface in fr.ens.biologie.genomique.aozan.tests.pooledsample: This interface define a test on a pooled sample.
PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.AozanCollector: Prefix for run data
PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.DemultiplexingCollector: Prefix for run data
PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector: Prefix for run data
PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector: Prefix for run data
PrimaryAnalysisMetricsCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This collector collect data from the PrimaryAnalysisMetrics.csv file if exists.
PrimaryAnalysisMetricsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.PrimaryAnalysisMetricsCollector
print() - Method in class fr.ens.biologie.genomique.aozan.RunData: Print the content of the object on standard output.
printValues() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Print dataset.
printValuesWithoutZero() - Method in class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Print dataset.
process() - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqThread
process() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesProcessThread
process(InputData) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.Step: Process input data.
process(InputData, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor
process(InputData, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2QCDataProcessor
process(InputData, RunConfiguration) - Method in interface fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DataProcessor: Process data.
process(InputData, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DiscoverNewIlluminaRunDataProcessor
process(InputData, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor
process(InputData, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.EndIlluminaRunDataProcessor
process(InputData, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.GuppyONTBasecallingDataProcessor
process(InputData, RunConfiguration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SyncDataProcessor
PROCESSED - fr.ens.biologie.genomique.aozan.aozan3.DataType.Category
PROCESSOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2QCDataProcessor
PROCESSOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Bcl2FastqIlluminaDemuxDataProcessor
PROCESSOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
PROCESSOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DiscoverNewIlluminaRunDataProcessor
PROCESSOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor
PROCESSOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.EndIlluminaRunDataProcessor
PROCESSOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.GuppyONTBasecallingDataProcessor
PROCESSOR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.IlluminaSyncDataProcessor
processResults() - Method in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesProcessThread: Process results after the end of the thread.
processSampleSheet(SampleSheet) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.AbstractIlluminaDemuxDataProcessor: Process sample sheet.
processSampleSheet(SampleSheet) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.BclConvertIlluminaDemuxDataProcessor
PROJECT_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.io.FastqSample: The Constant PROJECT_PREFIX.
ProjectComparator(RunData) - Constructor for class fr.ens.biologie.genomique.aozan.RunData.ProjectComparator: Constructor.
ProjectCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a projects count global test.
ProjectCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.ProjectCountGlobalTest: Public constructor.
ProjectStatisticsCollector - Class in fr.ens.biologie.genomique.aozan.collectors.stats: The class define a statistic collector on project's data to build a project summary table in qc report.
ProjectStatisticsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.stats.ProjectStatisticsCollector: Instantiates a new project statistics.
ProjectTest - Interface in fr.ens.biologie.genomique.aozan.tests.project: This interface define a test on lane.
PROVIDER_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.EmptyRunDataProvider
PROVIDER_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaProcessedRunDataProvider
PROVIDER_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.IlluminaRawRunDataProvider
PROVIDER_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.EmptyRunConfigurationProvider
PROVIDER_NAME - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.IlluminaSamplesheetRunConfigurationProvider
put(RunData) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set the key and values of a RunData object in the current RunData.
put(String, boolean) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key with a boolean value.
put(String, double) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key with a double value.
put(String, float) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key with a float value.
put(String, int) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key with an integer value.
put(String, long) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key with a long value.
put(String, long...) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key with an array of longs as value.
put(String, String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key.
put(String, String...) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key with an array of strings as value.
put(String, Collection<String>) - Method in class fr.ens.biologie.genomique.aozan.RunData: Set a key with a collection of strings as value.

Q

Q30PercentGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a Q30 percent global test.
Q30PercentGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.Q30PercentGlobalTest: Public constructor.
Q30PercentLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a Q30 percent lane test.
Q30PercentLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.Q30PercentLaneTest: Public constructor.
Q30PercentPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define test to compute the percent reads passing filter on all samples replica in run.
Q30PercentPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.Q30PercentPooledSampleTest: Public constructor.
Q30PercentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a percent Q30 sample test.
Q30PercentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.Q30PercentSampleTest: Public constructor.
QC - Class in fr.ens.biologie.genomique.aozan: This class is the main QC class.
QC - fr.ens.biologie.genomique.aozan.aozan3.DataType.Category
QC(Settings, String, String, String, File, String) - Constructor for class fr.ens.biologie.genomique.aozan.QC: Public constructor.
QC(Settings, String, String, String, File, String, SampleSheet) - Constructor for class fr.ens.biologie.genomique.aozan.QC: Public constructor.
QC(Settings, String, String, String, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.QC: Public constructor.
QC_COLLECTOR_NAMES - Static variable in class fr.ens.biologie.genomique.aozan.QC: QC output directory property key.
QC_CONF_FASTQC_ADAPTER_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Path to a specific adapter file, replace default file.
QC_CONF_FASTQC_BLAST_ARGUMENTS_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen blast arguments.
QC_CONF_FASTQC_BLAST_DB_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC blast database path.
QC_CONF_FASTQC_BLAST_ENABLE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC blast enable.
QC_CONF_FASTQC_BLAST_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC blast path.
QC_CONF_FASTQC_BLAST_USE_DOCKER_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Use Docker for Blast.
QC_CONF_FASTQC_CASAVA_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Illumina FASTQ format for FastQC.
QC_CONF_FASTQC_CONTAMINANT_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC contaminant file.
QC_CONF_FASTQC_EXPGROUP_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Use exponential base groups in graph.
QC_CONF_FASTQC_KEEP_ZIP_REPORT_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC, keep zip report file.
QC_CONF_FASTQC_KMER_SIZE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC kmer size.
QC_CONF_FASTQC_LIMITS_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Path to a specific limits file, replace default file.
QC_CONF_FASTQC_NANO_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: New option with FastQC 0.11.3 to nanopore technology, use Fast5 file instead of FastQ
QC_CONF_FASTQC_NOFILTER_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Filter bad Illumina FASTQ entry in FastQC.
QC_CONF_FASTQC_NOGROUP_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC nogroup.
QC_CONF_FASTQC_PROCESS_UNDETERMINED_SAMPLES_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC, process on undetermined indices samples, default at false.
QC_CONF_FASTQC_UNZIP_REPORT_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastQC, unzip report file.
QC_CONF_FASTQSCREEN_FASTQ_MAX_READS_PARSED_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen fastq max reads parsed.
QC_CONF_FASTQSCREEN_FASTQ_READS_PF_USED_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen fastq reads pf used.
QC_CONF_FASTQSCREEN_GENOMES_ALIAS_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen settings genomes alias path.
QC_CONF_FASTQSCREEN_GENOMES_DESC_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen settings genomes description path.
QC_CONF_FASTQSCREEN_GENOMES_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen genomes.
QC_CONF_FASTQSCREEN_GENOMES_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen settings genomes.
QC_CONF_FASTQSCREEN_MAPPER_ARGUMENTS_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen mapper argument.
QC_CONF_FASTQSCREEN_MAPPER_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen mapper.
QC_CONF_FASTQSCREEN_MAPPERS_INDEXES_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen settings mappers indexes path.
QC_CONF_FASTQSCREEN_MAPPING_IGNORE_PAIRED_END_MODE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen mapping ignore paired mode.
QC_CONF_FASTQSCREEN_MAPPING_SKIP_CONTROL_LANE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen mapping skip control lane.
QC_CONF_FASTQSCREEN_MAX_READ_LENGTH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen settings max read length.
QC_CONF_FASTQSCREEN_PERCENT_PROJECT_CONTAMINATION_THRESHOLD_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector project, fastqscreen xsl file
QC_CONF_FASTQSCREEN_PROCESS_UNDETERMINED_SAMPLES_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector FastqScreen, process on undetermined indices samples, default at false.
QC_CONF_FASTQSCREEN_PROJECT_XSL_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector project, fastqscreen xsl file
QC_CONF_FASTQSCREEN_XSL_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector fastqscreen xsl file.
QC_CONF_MULTIQC_USE_DOCKER_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Use Docker for MultiQC.
QC_CONF_READ_XML_COLLECTOR_USED_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector read xml collector used.
QC_CONF_THREADS_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector threads.
QC_CONF_UNDETERMINED_INDEXED_XSL_FILE_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Collector undetermined indexed xsl file.
QC_DATA_EXTENSION - Static variable in class fr.ens.biologie.genomique.aozan.Globals: QC data files extensions.
QC_OUTPUT_DIR - Static variable in class fr.ens.biologie.genomique.aozan.QC: QC output directory property key.
QC_REPORT_SAVE_RAW_DATA_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: QC report save raw data.
QC_REPORT_SAVE_REPORT_DATA_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: QC report save report data.
QC_REPORT_STYLESHEET_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: QC report stylesheet path.
QC_STEP_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: QC step.
QCReport - Class in fr.ens.biologie.genomique.aozan: This class generate the QC Report.
QCReport(QCReport) - Constructor for class fr.ens.biologie.genomique.aozan.QCReport: Copy constructor.
QCReport(RunData, List<GlobalTest>, List<LaneTest>, List<ProjectTest>, List<PooledSampleTest>, List<SampleTest>) - Constructor for class fr.ens.biologie.genomique.aozan.QCReport: Public constructor.
QCReportExporter - Class in fr.ens.biologie.genomique.aozan: This class export the QC Report in several formats.
QCReportExporter(QCReport) - Constructor for class fr.ens.biologie.genomique.aozan.QCReportExporter: Public constructor.
QualityMetricsCollector - Class in fr.ens.biologie.genomique.aozan.collectors.interop: This class collects run data by reading the QualityMetricsOut.bin in InterOp directory.
QualityMetricsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.interop.QualityMetricsCollector

R

RAW - fr.ens.biologie.genomique.aozan.aozan3.DataType.Category
RawClusterCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster global test.
RawClusterCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.RawClusterCountGlobalTest: Public constructor.
RawClusterCountLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a raw cluster test.
RawClusterCountLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.RawClusterCountLaneTest: Public constructor.
RawClusterCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test the sum on raw clusters on samples in a project.
RawClusterCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.RawClusterCountPooledSampleTest: Public constructor.
RawClusterCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define a test the sum on raw clusters on samples in a project.
RawClusterCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.RawClusterCountProjectTest: Public constructor.
RawClusterCountSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a raw clusters count test for samples.
RawClusterCountSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.RawClusterCountSampleTest: Public constructor.
RawClusterRecoveryCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test the maximum on raw clusters on samples in a project.
RawClusterRecoveryCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.RawClusterRecoveryCountPooledSampleTest: Public constructor.
RawClusterSDGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a raw cluster standard deviation global test.
RawClusterSDGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.RawClusterSDGlobalTest: Public constructor.
READ_DATA_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.ReadCollector
READ_ONLY_OUTPUT_FILES_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Change the output file rights.
ReadCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This class define a Collector for read?.xml files.
ReadCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.ReadCollector
readFileByLines(InputStream) - Static method in class fr.ens.biologie.genomique.aozan.util.FileUtils: Convert a file in string list.
Recipe - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a recipe.
Recipe(String, String, Configuration, GenericLogger) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.recipe.Recipe: Public constructor.
RecipeFinder - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a finder for recipe files.
RecipeFinder(Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder: Constructor.
RecipeFinder.RecipePath - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a result of the finder.
recipeName - Variable in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder.RecipePath
recipePath - Variable in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder.RecipePath
RECIPES_DIRECTORY_KEY - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.ConfigurationDefaults
RecipeXMLParser - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a recipe XML parser.
RecipeXMLParser(Configuration, Configuration, GenericLogger) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeXMLParser: Public constructor.
RecipeXMLParser(Configuration, GenericLogger) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeXMLParser: Public constructor.
RECOMPRESS_COMPRESSION_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Erase input after recompression.
RECOMPRESS_COMPRESSION_LEVEL_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Erase input after recompression.
RECOMPRESS_DELETE_ORIGINAL_FASTQ_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Erase input after recompression.
RECOMPRESS_STEP_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Recompression step.
RECOMPRESS_THREADS_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Erase input after recompression.
RecoverablePFClusterCountSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a recoverable passing filter clusters count test for samples.
RecoverablePFClusterCountSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.RecoverablePFClusterCountSampleTest: Public constructor.
RecoverablePFClusterPercentPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define test to compute the percent recoverable passing filter clusters for a project.
RecoverablePFClusterPercentPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.RecoverablePFClusterPercentPooledSampleTest: Public constructor.
RecoverablePFClusterPercentProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define test to compute the percent recoverable passing filter clusters for a project.
RecoverablePFClusterPercentProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.RecoverablePFClusterPercentProjectTest: Public constructor.
RecoverablePFClusterPercentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a recoverable passing filter clusters percent test for samples.
RecoverablePFClusterPercentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.RecoverablePFClusterPercentSampleTest: Public constructor.
RecoverableRawClusterCountSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a recoverable passing filter clusters count test for samples.
RecoverableRawClusterCountSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.RecoverableRawClusterCountSampleTest: Public constructor.
RecoverableRawClusterPercentPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define test to compute the percent recoverable raw clusters for a project.
RecoverableRawClusterPercentPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.RecoverableRawClusterPercentPooledSampleTest: Public constructor.
RecoverableRawClusterPercentProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The class define test to compute the percent recoverable raw clusters for a project.
RecoverableRawClusterPercentProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.RecoverableRawClusterPercentProjectTest: Public constructor.
RecoverableRawClusterPercentSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.sample: This class define a recoverable passing filter clusters percent test for samples.
RecoverableRawClusterPercentSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.sample.RecoverableRawClusterPercentSampleTest: Public constructor.
redemultiplex(File, String, List<String>, File) - Static method in class fr.ens.biologie.genomique.aozan.demux.ReDemux
ReDemux - Class in fr.ens.biologie.genomique.aozan.demux: This class allow to retrieve index from undetermined indices.
ReDemux(File, SampleSheet, File) - Constructor for class fr.ens.biologie.genomique.aozan.demux.ReDemux: Constructor.
redmux() - Method in class fr.ens.biologie.genomique.aozan.demux.ReDemux: Launch the re-demultiplexing.
reduce(String, Iterator<String>, List<String>, Reporter) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenPseudoMapReduce: Reducer Receive for each read list mapped genome Values first character represent the number of hits for a read : 1 or 2 (for several hits) and the end represent the name of reference genome.
registerThreadGroupLogger(ThreadGroup, Logger) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Register a logger for a thread group.
remove(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.DataStorageRegistry: Remove a data storage.
remove(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Remove a key from the Rundata.
removeIfExists(String) - Method in class fr.ens.biologie.genomique.aozan.RunData: Remove a key from the Rundata if the key exists.
removeThreadGroupLogger(ThreadGroup) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Remove a logger for a thread group.
removeTmpExtension(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.util.Utils: Remove the ".tmp" suffix of a string if exists.
REPORTS_DATA_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Report directory data path.
REPORTS_URL_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Report url.
reportToCSV(FastqSample, String) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult: Print table percent in format use by fastqscreen program with rounding value.
reportToHtml(FastqSample, RunData, String, File, File) - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.FastqScreenResult: Create report html file.
rewriteContaminantFinderMethod(boolean) - Static method in class fr.ens.biologie.genomique.aozan.fastqc.RuntimePatchFastQC: Add code at the beginning on the method.
RSync - Class in fr.ens.biologie.genomique.aozan.aozan3.util: This class define a synchronization tool based on the rsync command.
RSync(Path, Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.util.RSync
RSync(Path, Path, int) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.util.RSync
RSync(Path, Path, int, Collection<String>) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.util.RSync: Constructor.
RSync(Path, Path, Collection<String>) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.util.RSync
RTA_OUTPUT_DIR - Static variable in class fr.ens.biologie.genomique.aozan.QC: RTA output directory property key.
run(Path, Path, String, String, Path, String, String, String, boolean, String, String, String, int, int, boolean, boolean, GenericLogger) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.GuppyONTBasecallingDataProcessor
run(Path, Path, Path, String, String, Path, String, String, String, boolean, String, String, String, int, int, boolean, GenericLogger) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.DoradoONTBasecallingDataProcessor
RUN_DATA_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector: Prefix for run data
RunConfiguration - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a run configuration.
RunConfiguration() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.RunConfiguration: Default constructor.
RunConfiguration(RunConfiguration) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.RunConfiguration: Constructor.
RunConfigurationProvider - Interface in fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider: This interface define a run configuration provider.
RunConfigurationProviderService - Class in fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider: This class define a service to retrieve a RunConfigurationProvider
RunConfigurationProviderService() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.runconfigurationprovider.RunConfigurationProviderService: Private constructor.
runConfigurationToSettings(RunConfiguration) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.Aozan2Compatibility: Convert an Azoan 3 RunConfiguration object to an Aozan 2 Settings object.
RunData - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a run data.
RunData - Class in fr.ens.biologie.genomique.aozan: This class define a RunData object that contains all information generated by collectors.
RunData() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.RunData: Constructor for Gson
RunData() - Constructor for class fr.ens.biologie.genomique.aozan.RunData: Public constructor.
RunData(RunData) - Constructor for class fr.ens.biologie.genomique.aozan.RunData: Public constructor.
RunData(File) - Constructor for class fr.ens.biologie.genomique.aozan.RunData: Public constructor.
RunData.PooledSampleComparator - Class in fr.ens.biologie.genomique.aozan: This class define a comparator to order pooled samples.
RunData.ProjectComparator - Class in fr.ens.biologie.genomique.aozan: This class define a comparator to order projects.
RunDataFactory - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a RunData factory
RunDataGenerator - Class in fr.ens.biologie.genomique.aozan: This Class collect Data.
RunDataGenerator(List<Collector>, String, Map<String, String>) - Constructor for class fr.ens.biologie.genomique.aozan.RunDataGenerator: Public constructor.
RunDataProvider - Interface in fr.ens.biologie.genomique.aozan.aozan3.dataprovider: This interface define a run data provider.
RunDataProviderService - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprovider: This class define a service to retrieve a RunDataProvider
RunDataProviderService() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprovider.RunDataProviderService: Private constructor.
RunId - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a run run identifier.
RunId() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.RunId: Constructor for Gson
RunId(String) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.RunId: Public constructor.
RunId(String, String) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.RunId: Public constructor.
RunIdGenerator - Interface in fr.ens.biologie.genomique.aozan.aozan3: This class define an interface f that define how to create processor run data output names
RunIdStorage - Class in fr.ens.biologie.genomique.aozan.aozan3.legacy: This class allow to read and write processed run ids.
RunIdStorage(Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.legacy.RunIdStorage: Constructor.
RunInfoCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This collector collect data from the RunInfo.xml file, working with all RTA versions.
RunInfoCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.RunInfoCollector
runPatchFastQC() - Static method in class fr.ens.biologie.genomique.aozan.fastqc.RuntimePatchFastQC: Execute method who patch code from FastQC before call in Aozan.
runPatchFastQC(boolean) - Static method in class fr.ens.biologie.genomique.aozan.fastqc.RuntimePatchFastQC: Execute method who patch code from FastQC before call in Aozan.
RuntimePatchFastQC - Class in fr.ens.biologie.genomique.aozan.fastqc: This class redefine methods or constructors from FastQC to provide access to files in fastqc jar.
RuntimePatchFastQC() - Constructor for class fr.ens.biologie.genomique.aozan.fastqc.RuntimePatchFastQC

S

SAMPLE_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.io.FastqSample: The Constant SAMPLE_PREFIX.
SampleCountGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a samples count global test.
SampleCountGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.SampleCountGlobalTest: Public constructor.
SampleCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The Class SampleCountSampleTest.
SampleCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.SampleCountPooledSampleTest: Public constructor.
SampleCountProjectTest - Class in fr.ens.biologie.genomique.aozan.tests.project: The Class SampleCountProjectTest.
SampleCountProjectTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.project.SampleCountProjectTest: Public constructor.
SampleInPoolCountPooledSampleTest - Class in fr.ens.biologie.genomique.aozan.tests.pooledsample: The class define a test giving the number of sample in a pool.
SampleInPoolCountPooledSampleTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.pooledsample.SampleInPoolCountPooledSampleTest: Public constructor.
SAMPLESHEET - Static variable in class fr.ens.biologie.genomique.aozan.QC: Samplesheet path property key.
SAMPLESHEET_DATA_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector
SAMPLESHEET_FORMAT_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq samplesheet format.
SAMPLESHEET_GENERATOR_COMMAND_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq samplesheet generator command.
SAMPLESHEET_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq samplesheet path.
SAMPLESHEET_PREFIX_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Bcl2fastq samplesheet prefix filename.
SamplesheetCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This class define a Bcl2fastq samplesheet collector.
SamplesheetCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.SamplesheetCollector
SampleSheetConvertAction - Class in fr.ens.biologie.genomique.aozan.aozan3.action: This class define a sample sheet convert action.
SampleSheetConvertAction() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.action.SampleSheetConvertAction
SampleStatisticsCollector - Class in fr.ens.biologie.genomique.aozan.collectors.stats: The class define a statistic collector on sample's data to build a project summary table in qc report.
SampleStatisticsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector
SampleTest - Interface in fr.ens.biologie.genomique.aozan.tests.sample: This interface define sample test.
saveError(Aozan3Exception) - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter: Save error message.
saveFile(String, File, File) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter: Save file.
saveResultPart(FastqSample, RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.AbstractFastqCollector: Save rundata for a sample in a file in a qc report directory.
saveResultPart(FastqSample, RunData) - Method in class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector: No data file to save in UncompressCollector.
saveSampleSheet() - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter: Save the samplesheet.
saveSampleSheet() - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.IlluminaSampleSheetConverter
saveSampleSheet() - Method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.NanoporeSampleSheetConverter
saveUnknownAliases() - Method in class fr.ens.biologie.genomique.aozan.fastqscreen.GenomeAliases: Add the genome of the sample in the file which does correspondence with reference genome.
saveWarnings(List<String>, File, File) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter: Save warning message.
ScoreInterval - Class in fr.ens.biologie.genomique.aozan.util: This class define a score interval.
ScoreInterval() - Constructor for class fr.ens.biologie.genomique.aozan.util.ScoreInterval
select() - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Select the right model.
SEND_MAIL_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Send mail.
sendMail(EmailMessage) - Method in class fr.ens.biologie.genomique.aozan.aozan3.SendMail: Send an email with Aozan header and footer.
sendMail(String, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.SendMail: Send a message.
sendMail(String, String, boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.SendMail: Send a message.
SendMail - Class in fr.ens.biologie.genomique.aozan.aozan3: This class is used to send emails
SendMail(Configuration, GenericLogger) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.SendMail: Public constructor.
SequencerNames - Class in fr.ens.biologie.genomique.aozan.aozan3: This class allow to define names for sequencers.
SequencerNames(Configuration) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.SequencerNames: Constructor.
SequencerSource - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a sequencer source.
SequencerSourceFactory - Class in fr.ens.biologie.genomique.aozan.aozan3: This class define a sequencer source factory.
SequencerSourceFactory.IlluminaModel - Enum in fr.ens.biologie.genomique.aozan.aozan3: This enum defines Illumina sequencer models.
SequencerSourceFactory.Manufacturer - Enum in fr.ens.biologie.genomique.aozan.aozan3: This enum defines sequencer manufacturers.
set(Configuration) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Add all the keys and value of a Configuration object in this one.
set(String, boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value.
set(String, Number) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value.
set(String, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value.
setCompression(UnTar.Compression) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.Tar: Set the tar compression
setCompression(UnTar.Compression) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.UnTar: Set the tar compression
setCompressLogs(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Enable log files compression.
setCompressSequencingSummary(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Enable sequencing summary file compression.
setCompressTelemetry(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Enable telemetry file compression.
setDefaultLocale() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Globals: Set the default Local of the application
setFastqMerging(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Enable the FASTQ files merging.
setFooter(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Set the footer of the message.
setFromOtherConf(Configuration, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value from the value of another configuration.
setFromOtherConf(Configuration, String, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value from the value of another configuration.
setFromOtherConfIfExists(Configuration, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value from the value of another configuration.
setHeader(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Set the header of the message.
setIfNotExists(String, boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value if key does not exists.
setIfNotExists(String, Number) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value if key does not exists.
setIfNotExists(String, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Set a value if key does not exists.
setInterval(int, Interval) - Method in class fr.ens.biologie.genomique.aozan.util.ScoreInterval
setLoggerName(String) - Static method in class fr.ens.biologie.genomique.aozan.Aozan2Logger: Set the logger name.
setLogMerging(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.CopyAndMergeGuppyOutput: Enable the log files merging.
setLogOnly(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Create a new RunType object from the current object with a new log only setting.
setLogOnly(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Create a new RunType object from the current object with a new log only setting.
setPartialData(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType: Create a new RunType object from the current object with a new partial data setting.
setPartialData(boolean) - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData: Create a new RunType object from the current object with a new partial data setting.
setTemplate(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Set the template of the message.
setTemplateFromFile(Path) - Method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Set the template from a resource file.
setTemplateFromResource(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Set the template from a resource file.
Settings - Class in fr.ens.biologie.genomique.aozan: This class define constants to keys of configuration Aozan file.
Settings(Map<String, String>) - Constructor for class fr.ens.biologie.genomique.aozan.Settings: Public constructor.
showErrorMessageAndExit(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Common: Show a message and then exit.
showMessageAndExit(String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.Common: Show a message and then exit.
SimpleDataTypeFilter - Class in fr.ens.biologie.genomique.aozan.aozan3.datatypefilter: This class define a DataTypeFilter that require a specific DataType.
SimpleDataTypeFilter(DataType) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.SimpleDataTypeFilter: Consctructor.
SimpleProcessResult - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define a simple ProcessResult.
SimpleProcessResult(RunData, EmailMessage) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SimpleProcessResult: Constructor.
SimpleProcessResult(Set<RunData>, EmailMessage) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SimpleProcessResult: Constructor.
size() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Return the size of the configuration.
size() - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.InputData: Get the size of the collection.
size() - Method in class fr.ens.biologie.genomique.aozan.RunData: Get the number of entries in RunData.
stackTraceToString(Throwable) - Static method in class fr.ens.biologie.genomique.aozan.util.StringUtils: Convert a stack trace of an exception into a string.
StatisticsCollector - Class in fr.ens.biologie.genomique.aozan.collectors: The class define a abstract statistics collector.
StatisticsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.StatisticsCollector
StatisticsUtils - Class in fr.ens.biologie.genomique.aozan.util: This class contains statistics methods, using the class DescriptiveStatistics from commons.apache.math.
StatisticsUtils() - Constructor for class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Public constructor with a empty dataset.
StatisticsUtils(Collection<? extends Number>) - Constructor for class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Public constructor, build a list of values used for compute statistics.
StatisticsUtils(List<? extends Number>) - Constructor for class fr.ens.biologie.genomique.aozan.util.StatisticsUtils: Public constructor, build a list of values used for compute statistics.
Step - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a step of the recipe.
Step(Recipe, String, String, String, Configuration, RunConfigurationProvider, RunIdGenerator) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.recipe.Step: Constructor.
StepsXMLParser - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a XML parser for steps.
Storages - Class in fr.ens.biologie.genomique.aozan: This class define storage for FastQ Screen.
StoragesXMLParser - Class in fr.ens.biologie.genomique.aozan.aozan3.recipe: This class define a XML parser for storages.
StringUtils - Class in fr.ens.biologie.genomique.aozan.util: The Class StringUtils.
StringUtils() - Constructor for class fr.ens.biologie.genomique.aozan.util.StringUtils
submitSequence(String) - Method in class fr.ens.biologie.genomique.aozan.fastqc.OverrepresentedSequencesBlast: Submit a sequence to blast
SUBSET_FASTQ_FILENAME_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.io.FastqSample
SubsetFastqCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This class manages the creation of subset fastq files for contamination research.
SubsetFastqCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqCollector
SubsetFastqThread - Class in fr.ens.biologie.genomique.aozan.collectors: The class define a class for a thread that create a temporary partial fastq file, with fixed reads (200 000) to use for contamination research.
SubsetFastqThread(FastqSample, long, long, int, int, int) - Constructor for class fr.ens.biologie.genomique.aozan.collectors.SubsetFastqThread: Thread constructor.
sync() - Method in class fr.ens.biologie.genomique.aozan.aozan3.util.RSync: Synchronize.
sync(Path, Path) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.IlluminaSyncDataProcessor
sync(Path, Path) - Method in class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SyncDataProcessor
SYNC_CONTINUOUS_SYNC_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Synchronization continuous.
SYNC_CONTINUOUS_SYNC_MIN_AGE_FILES_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Synchronization continuous minimum ages files.
SYNC_EXCLUDE_CIF_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Synchronization exclude cif files.
SYNC_SPACE_FACTOR_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Synchronization space factor.
SYNC_STEP_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Synchronization step.
SyncDataProcessor - Class in fr.ens.biologie.genomique.aozan.aozan3.dataprocessor: This class define an Illumina synchronization data processor.
SyncDataProcessor() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.dataprocessor.SyncDataProcessor

T

Tar - Class in fr.ens.biologie.genomique.aozan.aozan3.util: This class allow to create tar files.
Tar(Path, Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.util.Tar: Constructor.
TAR - fr.ens.biologie.genomique.aozan.aozan3.DataLocation.Format
TAR_BZ2 - fr.ens.biologie.genomique.aozan.aozan3.DataLocation.Format
TAR_GZ - fr.ens.biologie.genomique.aozan.aozan3.DataLocation.Format
TechnologyDataTypeFilter - Class in fr.ens.biologie.genomique.aozan.aozan3.datatypefilter: This class define a DataTypeFilter that require or not partial data..
TechnologyDataTypeFilter(DataType.SequencingTechnology) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.TechnologyDataTypeFilter: Constructor.
TEMP_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The prefix for temporary files.
TEMP_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The prefix for temporary files.
TemplateEmailMessage - Class in fr.ens.biologie.genomique.aozan.aozan3: This class allow to generate EmailMessage from templates.
TemplateEmailMessage() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Public constructor.
TemplateEmailMessage(Configuration) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Public constructor.
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractSimpleGlobalTest
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.ClusterDensityGlobalTest
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.ClusterDensityPFGlobalTest
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.ErrorRateGlobalTest
test(RunData) - Method in interface fr.ens.biologie.genomique.aozan.tests.global.GlobalTest: Do a test.
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.OccupancyPercentGlobalTest
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.ProjectCountGlobalTest
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.Q30PercentGlobalTest
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.SampleCountGlobalTest
test(RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.UndeterminedClusterPercentGlobalTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedExceptRefPercentPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenMappedPercentPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenReportPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.FastQScreenSampleOvercontaminationCountPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.InProjectPercentPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.InRunPercentPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFBaseMeanQualityScorePooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.PFPercentPooledSampleTest
test(RunData, int) - Method in interface fr.ens.biologie.genomique.aozan.tests.pooledsample.PooledSampleTest: Do a test.
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.Q30PercentPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RecoverablePFClusterPercentPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.RecoverableRawClusterPercentPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.SampleInPoolCountPooledSampleTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.FastQScreenReportProjectTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.MultiQCReportProjectTest
test(RunData, int) - Method in interface fr.ens.biologie.genomique.aozan.tests.project.ProjectTest: Do a test.
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.RecoverablePFClusterPercentProjectTest
test(RunData, int) - Method in class fr.ens.biologie.genomique.aozan.tests.project.RecoverableRawClusterPercentProjectTest
test(RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest
test(RunData, int, boolean, int) - Method in interface fr.ens.biologie.genomique.aozan.tests.lane.LaneTest: Do a test.
test(RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterPercentLaneTest
test(RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhasingPrephasingPercentLaneTest
test(RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhiXAlignPercentLaneTest
test(RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PhiXRawClusterCountLaneTest
test(RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Q30PercentLaneTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractFastQCSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.BasePFMeanQualityScoreSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.ClusterRecoveryReportSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenReportSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.InLanePercentSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.PFPercentSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.Q30PercentSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverablePFClusterPercentSampleTest
test(RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.RecoverableRawClusterPercentSampleTest
test(RunData, int, int, int) - Method in interface fr.ens.biologie.genomique.aozan.tests.sample.SampleTest: Do a test.
TEST_KEY_ENABLED_SUFFIX - Static variable in class fr.ens.biologie.genomique.aozan.QC
TEST_KEY_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.QC
TestConfiguration - Class in fr.ens.biologie.genomique.aozan.tests: This class define the configuration of a test.
TestConfiguration(Settings, String, Map<String, String>) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestConfiguration: Public constructor.
TestConfiguration(Map<String, String>) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestConfiguration: Public constructor.
testIndexedRead() - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest: Test if indexed read test must return a score >=0.
testIndexedRead() - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest: Test if indexed read test must return a score >=0.
testIndexedRead() - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest: Test if indexed read test must return a score >=0.
TestResult - Class in fr.ens.biologie.genomique.aozan.tests: This class define a test result.
TestResult(int, Number) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestResult: Public constructor.
TestResult(int, Number, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestResult: Public constructor.
TestResult(int, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestResult: Public constructor.
TestResult(int, String, String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestResult: Public constructor.
TestResult(Number) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestResult: Public constructor.
TestResult(Number, boolean) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestResult: Public constructor.
TestResult(String) - Constructor for class fr.ens.biologie.genomique.aozan.tests.TestResult: Public constructor.
TileMetricsCollector - Class in fr.ens.biologie.genomique.aozan.collectors.interop: This class collects run data by reading the TileMetricsOut.bin in InterOp directory.
TileMetricsCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.interop.TileMetricsCollector
TMP_DIR - Static variable in class fr.ens.biologie.genomique.aozan.QC: Temporary directory property key.
TMP_PATH_KEY - Static variable in class fr.ens.biologie.genomique.aozan.Settings: Directory tmp path.
toDocument() - Method in class fr.ens.biologie.genomique.aozan.QCReport: Get Report as a XML Document.
toEmailMessage(long, String, Map<String, String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Generate EmailMessage object.
toEmailMessage(String, Map<String, String>) - Method in class fr.ens.biologie.genomique.aozan.aozan3.TemplateEmailMessage: Generate EmailMessage object.
toJson() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage: Serialize the object into a JSON string
toMap() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration: Convert the configuration as a Map.
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.Configuration
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataLocation
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataStorage
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.DataType
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.CategoryDataTypeFilter
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.MultiDataTypeFilter
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.PartialDataTypeFilter
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.SimpleDataTypeFilter
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.datatypefilter.TechnologyDataTypeFilter
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.recipe.RecipeFinder.RecipePath
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunData
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.RunId
toString() - Method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSource
toString() - Method in enum fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.IlluminaModel
toString() - Method in enum fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.Manufacturer
toString() - Method in class fr.ens.biologie.genomique.aozan.collectors.CollectorConfiguration
toString() - Method in class fr.ens.biologie.genomique.aozan.collectors.stats.EntityStat
toString() - Method in class fr.ens.biologie.genomique.aozan.fastqc.BlastContaminantHit
toString() - Method in class fr.ens.biologie.genomique.aozan.io.FastqSample
toString() - Method in class fr.ens.biologie.genomique.aozan.RunData
toString() - Method in class fr.ens.biologie.genomique.aozan.tests.TestConfiguration
toString() - Method in class fr.ens.biologie.genomique.aozan.util.DoubleInterval
toString() - Method in class fr.ens.biologie.genomique.aozan.util.LongInterval
toXML() - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Create the QC report as an XML String.
transformScore(int, RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest: Transform the score.
transformScore(int, RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedPercentSampleTest: Transform the score : if genome of sample is the same as reference genome.
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.AbstractSimpleGlobalTest: Transform the value.
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.BaseCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.CycleCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.LaneCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.LoadingConcentrationPercentGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanPFClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanPhiXRawClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.MeanRawClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianPFClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianPhiXRawClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.MedianRawClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.NonIndexedBaseCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterPercentGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.PFClusterSDGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXAlignPercentGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.PhiXRawClusterSDGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.RawClusterCountGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.global.RawClusterSDGlobalTest
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.pooledsample.AbstractSimpleSampleTest: Transform the value.
transformValue(Number, RunData) - Method in class fr.ens.biologie.genomique.aozan.tests.project.AbstractSimpleProjectTest: Transform the value.
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.AbstractSimpleLaneTest: Transform the value.
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ClusterDensityPFLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle100ErrorRateLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle20IntensityPercentLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle35ErrorRateLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.Cycle75ErrorRateLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.DensityLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.ErrorRateLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.OccupancyPercentLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.PFClusterCountLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.RawClusterCountLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.lane.YieldPFLaneTest
transformValue(Number, RunData, int, boolean, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.FastQScreenMappedExceptRefGenomeSampleTest
transformValue(Number, RunData, int, int, int) - Method in class fr.ens.biologie.genomique.aozan.tests.sample.AbstractSimpleSampleTest: Transform the value.

U

UNDETERMINED_DIR_NAME - Static variable in class fr.ens.biologie.genomique.aozan.io.FastqSample: The Constant UNDETERMINED_DIR_NAME.
UNDETERMINED_PREFIX - Static variable in class fr.ens.biologie.genomique.aozan.io.FastqSample: The Constant UNDETERMINED_PREFIX.
UNDETERMINED_SAMPLE - Static variable in class fr.ens.biologie.genomique.aozan.collectors.stats.SampleStatisticsCollector
UndeterminedClusterPercentGlobalTest - Class in fr.ens.biologie.genomique.aozan.tests.global: This class define a projects count global test.
UndeterminedClusterPercentGlobalTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.global.UndeterminedClusterPercentGlobalTest: Public constructor.
UndeterminedIndexesCollector - Class in fr.ens.biologie.genomique.aozan.collectors: This class allow to collect information about the undetermined indices that can be recovered.
UndeterminedIndexesCollector() - Constructor for class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesCollector
UndeterminedIndexesProcessThread - Class in fr.ens.biologie.genomique.aozan.collectors: This class allow to process the undetermined fastq file of a lane to extract indices that can be recovered.
UndeterminedIndexesProcessThread(RunData, FastqSample, File, File) - Constructor for class fr.ens.biologie.genomique.aozan.collectors.UndeterminedIndexesProcessThread: Constructor.
unknownSequencerSource() - Static method in class fr.ens.biologie.genomique.aozan.aozan3.SequencerSource
unlock() - Method in class fr.ens.biologie.genomique.aozan.aozan3.legacy.AozanLock: Remove the lock file.
UnTar - Class in fr.ens.biologie.genomique.aozan.aozan3.util: This class allow to create untar archives.
UnTar(Path, Path) - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.util.UnTar: Constructor.
UnTar.Compression - Enum in fr.ens.biologie.genomique.aozan.aozan3.util
Utils - Class in fr.ens.biologie.genomique.aozan.aozan3.util: This class contains some utility methods.
Utils() - Constructor for class fr.ens.biologie.genomique.aozan.aozan3.util.Utils

V

valueOf(String) - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.DataLocation.Format: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.DataType.Category: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.DataType.SequencingTechnology: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.IlluminaModel: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.Manufacturer: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.util.UnTar.Compression: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput.Bcl2FastqVersion: Returns the enum constant of this type with the specified name.
values() - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.DataLocation.Format: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.DataType.Category: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.DataType.SequencingTechnology: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.IlluminaModel: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.SequencerSourceFactory.Manufacturer: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.aozan.aozan3.util.UnTar.Compression: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum fr.ens.biologie.genomique.aozan.illumina.Bcl2FastqOutput.Bcl2FastqVersion: Returns an array containing the constants of this enum type, in the order they are declared.

W

warn(RunData, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log a warning message.
warn(RunId, String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log a warning message.
warn(GenericLogger, RunData, String) - Static method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log a warning message.
warn(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.log.Aozan3Logger: Log a warning message.
warningFile - Variable in class fr.ens.biologie.genomique.aozan.aozan3.samplesheetconverter.AbstractSampleSheetConverter
WEBSITE_URL - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: Application Website url.
WEBSITE_URL - Static variable in class fr.ens.biologie.genomique.aozan.Globals: Application Website url.
WELCOME_MSG - Static variable in class fr.ens.biologie.genomique.aozan.aozan3.Globals: The welcome message.
WELCOME_MSG - Static variable in class fr.ens.biologie.genomique.aozan.Globals: The welcome message.
withAnalyteType(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the analyte type.
withChemistryType(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the chemistry type.
withFlowcellReference(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the flowcell reference.
withKitReference(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the kit reference.
withModelType(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the model type.
withModification(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter that allow models that handle a modification.
withNoModification() - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter that reject models that handle modifications.
withPoreType(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the pore type.
withSamplingFrequency(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the sampling frequency.
withTranslocationSpeed(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the translocation speed.
withVersion(String) - Method in class fr.ens.biologie.genomique.aozan.aozan3.nanopore.BasecallingModelSelector: Add a filter based on the version of the model.
writeRawData(File) - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Write the raw data of the QC.
writeRawData(String) - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Write the raw data of the QC.
writeReport(InputStream, File) - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Write the report usually in HTML) in a file.
writeReport(String, String) - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Write the report usually in HTML) in a file.
writeTable(HTMLReportArchive, TableModel) - Method in class fr.ens.biologie.genomique.aozan.fastqc.AbstractQCModuleAozan
writeTextTable(HTMLReportArchive, TableModel) - Method in class fr.ens.biologie.genomique.aozan.fastqc.AbstractQCModuleAozan
writeXhtmlTable(HTMLReportArchive, TableModel) - Method in class fr.ens.biologie.genomique.aozan.fastqc.AbstractQCModuleAozan
writeXMLReport(File) - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Write the XML in a file.
writeXMLReport(String) - Method in class fr.ens.biologie.genomique.aozan.QCReportExporter: Write the XML in a file.

X

XMLUtilsParser - Class in fr.ens.biologie.genomique.aozan.util: The class define utility methods to extract information to a xml with the good type.
XMLUtilsParser() - Constructor for class fr.ens.biologie.genomique.aozan.util.XMLUtilsParser
XMLUtilsWriter - Class in fr.ens.biologie.genomique.aozan.util: The class implements common action to create control quality report.
XMLUtilsWriter() - Constructor for class fr.ens.biologie.genomique.aozan.util.XMLUtilsWriter
XZ - fr.ens.biologie.genomique.aozan.aozan3.util.UnTar.Compression

Y

YieldLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a yield lane test.
YieldLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.YieldLaneTest: Public constructor.
YieldPFLaneTest - Class in fr.ens.biologie.genomique.aozan.tests.lane: This class define a yield passing filter lane test.
YieldPFLaneTest() - Constructor for class fr.ens.biologie.genomique.aozan.tests.lane.YieldPFLaneTest: Public constructor.

Z

ZIP - fr.ens.biologie.genomique.aozan.aozan3.DataLocation.Format

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