- P_VAL_CUTOFF - Static variable in class biolockj.Constants
-
Config
property "r.pvalCutoff" defines the p-value cutoff for significance
- P_VALS_NP - Static variable in class biolockj.module.report.r.R_CalculateStats
-
Non parametric p-value identifier: "nonParametricPvals"
- P_VALS_NP_ADJ - Static variable in class biolockj.module.report.r.R_CalculateStats
-
Non parametric adjusted p-value identifier: "adjNonParPvals"
- P_VALS_PAR - Static variable in class biolockj.module.report.r.R_CalculateStats
-
Parametric p-value identifier: "parametricPvals"
- P_VALS_PAR_ADJ - Static variable in class biolockj.module.report.r.R_CalculateStats
-
Parametric adjusted p-value identifier: "adjParPvals"
- PARAM - Static variable in class biolockj.module.diy.GenMod
-
Config
property: "genMod.param"
- parameters - Variable in class biolockj.launch.LaunchProcess
-
- parentTaxaLevel(String) - Static method in class biolockj.util.TaxaUtil
-
Get parent level name of the given level parameter.
- parseCountTable(File) - Static method in class biolockj.util.BioLockJUtil
-
Read in BioLockJ count table, each inner lists represents 1 line from the file.
Each cell in the tab delimited file is stored as 1 element in the inner lists.
- ParsedSample - Class in biolockj.node
-
- ParsedSample(OtuNode) - Constructor for class biolockj.node.ParsedSample
-
Construct a new ParsedSample with it's 1st OtuNode.
- ParserModule - Interface in biolockj.module.implicit.parser
-
This interface defines the required methods to parse ClassifierModule output.
- ParserModuleImpl - Class in biolockj.module.implicit.parser
-
- ParserModuleImpl() - Constructor for class biolockj.module.implicit.parser.ParserModuleImpl
-
- parseRow(String, boolean) - Method in class biolockj.module.implicit.ImportMetadata
-
- parseSample(File) - Method in class biolockj.module.implicit.parser.wgs.Kraken2Parser
-
- parseSample(File) - Method in class biolockj.module.implicit.parser.wgs.KrakenParser
-
Construct a new KrakenNode
- parseSamples() - Method in interface biolockj.module.implicit.parser.ParserModule
-
- parseSamples() - Method in class biolockj.module.implicit.parser.ParserModuleImpl
-
- parseSamples() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser
-
- parseSamples() - Method in class biolockj.module.implicit.parser.r16s.RdpParser
-
- parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser
-
- parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Kraken2Parser
-
- parseSamples() - Method in class biolockj.module.implicit.parser.wgs.KrakenParser
-
- parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Metaphlan2Parser
-
- partiallyInitialize(File) - Static method in class biolockj.Config
-
- PASS - Static variable in class biolockj.util.ValidationUtil
-
- passEnvironmentVarVals(ScriptModule) - Static method in class biolockj.util.BashScriptBuilder
-
- PASSWORD - Static variable in class biolockj.util.RuntimeParamUtil
-
Change password runtime parameter switch: "-password"
- PASSWORD_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- PathMapper - Interface in biolockj.util.paths
-
- pathVariableVals(ScriptModule) - Static method in class biolockj.util.BashScriptBuilder
-
Get the script lines to assign values to the common directories.
- PathwayUtil - Class in biolockj.util
-
This utility helps work HumanN2 pathway abundance data.
- pauseToRead() - Static method in class biolockj.launch.Launcher
-
- PDF_EXT - Static variable in class biolockj.Constants
-
BioLockJ PDF file extension: ".pdf"
- PDF_EXT - Static variable in class biolockj.module.BioModuleImpl
-
BioLockJ PDF file extension constant: ".pdf"
- PearMergeReads - Class in biolockj.module.seq
-
- PearMergeReads() - Constructor for class biolockj.module.seq.PearMergeReads
-
- PHYLUM - Static variable in class biolockj.Constants
-
- PHYLUM_DELIM - Static variable in class biolockj.node.OtuNodeImpl
-
Standard classifier output level delimiter for PHYLUM
- PICK_OTU_SCRIPT - Static variable in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier
-
Closed reference OTU picking script: "pick_closed_reference_otus.py"
- PICK_OTU_SCRIPT - Static variable in class biolockj.module.classifier.r16s.QiimeDeNovoClassifier
-
De novo OTU picking script: "pick_de_novo_otus.py"
- PICK_OTU_SCRIPT - Static variable in class biolockj.module.classifier.r16s.QiimeOpenRefClassifier
-
Open reference OTU picking script: "pick_open_reference_otus.py"
- Pipeline - Class in biolockj
-
This class initializes and executes each
BioModule
configured for execution.
BioModule
s that generate scripts are monitored until all scripts are complete, before moving
on to the next module.
- PIPELINE_COPY_FILES - Static variable in class biolockj.Constants
-
Config
property: "pipeline.copyInput"
- PIPELINE_DEFAULT_PROPS - Static variable in class biolockj.Constants
-
Config
String property: "pipeline.defaultProps"
- PIPELINE_DESC - Static variable in class biolockj.Constants
-
Config
property to allow a free-hand description to a pipeline: "pipeline.desc" TODO:
needs to be implemented.
- PIPELINE_ENV - Static variable in class biolockj.Constants
-
Config
String property: "pipeline.env"
- PIPELINE_ENV_AWS - Static variable in class biolockj.Constants
-
- PIPELINE_ENV_CLUSTER - Static variable in class biolockj.Constants
-
- PIPELINE_ENV_LOCAL - Static variable in class biolockj.Constants
-
Config
option for property:
"pipeline.env"
Used to indicate running on a local machine (laptop, etc): "local"
- PIPELINE_ENV_VARS - Static variable in class biolockj.Constants
-
- PIPELINE_ENV_VARS_DESC - Static variable in class biolockj.Constants
-
- PIPELINE_HUMANN2_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
Pipeline input file type indicating the file is Humann2 generated
- PIPELINE_LOCATION_KEY - Static variable in class biolockj.Constants
-
Indicator for related programs (bash code, sheepdog_testing_suite) of the pipelines path: "Pipeline root directory: "
- PIPELINE_LOG_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_NAME - Static variable in class biolockj.Constants
-
Config
property to assign a name to a pipeline: "pipeline.name" TODO: needs to be
implemented.
- PIPELINE_NORMAL_TAXA_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_PAIRED_READS_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_PARSER_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_PRIVS - Static variable in class biolockj.Constants
-
Config
property: "pipeline.permissions"
- PIPELINE_R_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_SEQ_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_STATS_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_STATUS - Static variable in class biolockj.util.SummaryUtil
-
- PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
-
- PIPELINE_USE_EVARS - Static variable in class biolockj.Constants
-
- PIPELINE_USE_EVARS_DESC - Static variable in class biolockj.Constants
-
- PipelineFormationException - Exception in biolockj.exception
-
PipelineFormationException is thrown when there is a problem in setting up the modules to run.
- PipelineFormationException(String) - Constructor for exception biolockj.exception.PipelineFormationException
-
- pipelineInputContainsOtuSummary() - Static method in class biolockj.module.report.JsonReport
-
Check pipeline input to see if OTU summary file is the only pipeline input file.
- pipelineInputType(String) - Static method in class biolockj.util.BioLockJUtil
-
Convenience method to check pipeline input file type.
- pipelineInternalInputDir() - Static method in class biolockj.util.BioLockJUtil
-
Return the pipeline input directory
- pipelineName() - Static method in class biolockj.Config
-
Get the current pipeline name (root folder name)
- pipelinePath() - Static method in class biolockj.Config
-
Get the current pipeline absolute directory path (root folder path)
- PipelineScriptException - Exception in biolockj.exception
-
PipelineScriptException is thrown by
BashScriptBuilder
if errors occur writing MASTER & WORKER
scripts.
- PipelineScriptException(ScriptModule, boolean, String) - Constructor for exception biolockj.exception.PipelineScriptException
-
Create standard error to throw writing MASTER & WORKER bash scripts.
- PipelineScriptException(ScriptModule, String) - Constructor for exception biolockj.exception.PipelineScriptException
-
Create standard error to throw if problems occur generating pipeline bash scripts.
- PipelineScriptException(String) - Constructor for exception biolockj.exception.PipelineScriptException
-
Create a standard exception message.
- PipelineUtil - Class in biolockj.pipelines
-
- PipelineUtil() - Constructor for class biolockj.pipelines.PipelineUtil
-
- piplineHasSeqInput() - Static method in class biolockj.util.SeqUtil
-
Return TRUE if pipeline input files are sequence files.
- PLS_USE_INSTALL - Static variable in class biolockj.launch.LaunchProcess
-
- poll(ScriptModule) - Static method in class biolockj.Pipeline
-
The
ScriptModule.getScriptDir()
will contain one main script and one ore more worker
scripts.
An empty file with appended to the script name is created when execution
begins.
If successful, an empty file with appended to the script name is created.
Upon failure, an empty file with appended to the script name is created.
Script status is polled each minute, determining status by counting indicator files.
Log
outputs the # of started, failed, and successful scripts (if any change).
Log
repeats the previous message every 10 minutes if no status change is detected.
- populateInBetweenTaxa() - Method in class biolockj.node.OtuNodeImpl
-
Populate missing OTUs if top level taxa is defined and there is a level gap between the top level and the bottom
level.
- POS_INTEGER_TYPE - Static variable in class biolockj.Properties
-
- PRECHECK_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- PRECHECK_COMPLETE - Static variable in class biolockj.Constants
-
Name of the file created in the BioModule root directory to indicate the precheck
process encountered an error (if running in precheck mode): "precheckComplete"
- PRECHECK_FAILED - Static variable in class biolockj.Constants
-
Name of the file created in the BioModule root directory to indicate the precheck
process has completed (if running in precheck mode): "precheckFailed"
- PRECHECK_FLAG - Static variable in class biolockj.util.RuntimeParamUtil
-
Flag argument; if present, BioLockJ will stop after checkDependencies step.
- PRECHECK_STARTED - Static variable in class biolockj.Constants
-
Name of the file created in the BioModule root directory to indicate the precheck
process has started (if running in precheck mode): "precheckStarted"
- printActionOptions() - Method in class biolockj.launch.LaunchProcess
-
- printArgsDescriptions() - Static method in class biolockj.util.RuntimeParamUtil
-
Print arg descriptions
TODO: PROBLEMATIC APPROACH TO SHOW ARGS BY PRINTING VARIABLES IN THIS METHOD
- printHelp() - Static method in class biolockj.launch.LaunchProcess
-
Print the help to standard err.
- printHelp(PrintStream) - Static method in class biolockj.launch.LaunchProcess
-
Print the help menu.
- printInfo() - Method in class biolockj.launch.LaunchProcess
-
- printLongFormList(Collection<?>) - Static method in class biolockj.util.BioLockJUtil
-
Print collection one item per line.
- printPipeDir() - Method in class biolockj.launch.LaunchProcess
-
Print the path to the pipeline root to standard out.
- printPipelineStatus(int) - Method in class biolockj.launch.LaunchProcess
-
Show the status the just-launched pipeline.
- printRuntimeArgs(String[]) - Static method in class biolockj.util.RuntimeParamUtil
-
Print the runtime args to System.out or using the Logger based on useSysOut parameter.
- printStatus(String, boolean) - Static method in class biolockj.launch.ProgressUtil
-
Print a message to the screen.
- printVersion() - Static method in class biolockj.launch.LaunchProcess
-
Print the version to standard out.
- PROCESSED - Static variable in class biolockj.Constants
-
File suffix appended to processed samples in the module output directory: "_reported.tsv"
- Processor - Class in biolockj
-
- Processor() - Constructor for class biolockj.Processor
-
Empty constructor to facilitate subprocess creation
- Processor.Subprocess - Class in biolockj
-
Class used to submit processes on their own Thread.
- ProgressMsgDemo - Class in biolockj.launch
-
- ProgressMsgDemo() - Constructor for class biolockj.launch.ProgressMsgDemo
-
- ProgressUtil - Class in biolockj.launch
-
This utility controls the information printed to the screen during launch.
- ProgressUtil() - Constructor for class biolockj.launch.ProgressUtil
-
Utility class, no instantiation.
- PROJ_ARG - Static variable in class biolockj.launch.LaunchProcess
-
- PROJECT_DEFAULT_PROPS - Static variable in class biolockj.Constants
-
Config
String property: "project.defaultProps"
Set file path of default property file.
- PROJECT_DESC - Static variable in class biolockj.Constants
-
Config
property to assign a free-hand to a project: "project.description" TODO: needs to be
implemented.
- PROJECT_NAME - Static variable in class biolockj.Constants
-
Config
property to assign a name to a project: "project.name" TODO: needs to be
implemented.
- promptChange() - Static method in exception biolockj.exception.ConfigException
-
- propDescModule(String, String) - Static method in class biolockj.api.BioLockJ_API
-
- Properties - Class in biolockj
-
Load properties defined in the BioLockJ configuration file, including inherited properties from project.defaultProps
- Properties() - Constructor for class biolockj.Properties
-
Default constructor.
- Properties(Properties) - Constructor for class biolockj.Properties
-
- propInfo() - Static method in class biolockj.api.BioLockJ_API
-
For each of the properties registered to the Properties class,
report the property name, type, description and default value.
- props - Static variable in class biolockj.Config
-
- PROPS_EXT - Static variable in class biolockj.Constants
-
BioLockJ properties file extension: ".properties"
- propTypeModule(String, String) - Static method in class biolockj.api.BioLockJ_API
-
Returns a string describing the format type that required for the value of the property given.
- propValue(String, String, BioModule) - Static method in class biolockj.api.BioLockJ_API
-
Returns the value for that property (first String)
If a second argument is given, it is assumed to be the primary config file.
- propValue(String, BioModule) - Static method in class biolockj.api.BioLockJ_API
-
- propValue(String) - Static method in class biolockj.api.BioLockJ_API
-
- PURE_DOCKER_PIPELINE_DIR - Static variable in class biolockj.util.DockerUtil
-
When running in pure docker to do the initial setup, use this pipelines dir: "/workspace/pipelines"
- purgeEfsData() - Static method in class biolockj.util.NextflowUtil
-
Purge EFS data based on pipeline Config.