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P

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
ParserModules create and store one ParsedSample, with OTU assignments and counts, for each sample.
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
Parser BioModules read ClassifierModule output to build standardized OTU count tables.
ParserModuleImpl() - Constructor for class biolockj.module.implicit.parser.ParserModuleImpl
 
parseRow(String, boolean) - Method in class biolockj.module.implicit.ImportMetadata
Method called to parse a row from the metadata file, where Config."metadata.columnDelim" separates columns.
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
Parse ClassifierModule output to build ParsedSamples.
parseSamples() - Method in class biolockj.module.implicit.parser.ParserModuleImpl
 
parseSamples() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser
Parse lowest level QiimeClassifier report in the input directory.
parseSamples() - Method in class biolockj.module.implicit.parser.r16s.RdpParser
Parse all RdpClassifier reports in the input directory.
Build an RdpNode for each line.
If RdpParser.isValid(OtuNode),
Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.
parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser
To parse the taxonomy level reports output by Humann2Classifier.
parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Kraken2Parser
Parse all Kraken2Classifier reports in the input directory.
Cache the leaf counts Build an Kraken2Node for each line.
If ParserModuleImpl.isValid(OtuNode),
Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.
parseSamples() - Method in class biolockj.module.implicit.parser.wgs.KrakenParser
Parse all KrakenClassifier reports in the input directory.
Cache the leaf counts Build an KrakenNode for each line.
If ParserModuleImpl.isValid(OtuNode),
Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.
parseSamples() - Method in class biolockj.module.implicit.parser.wgs.Metaphlan2Parser
To parse the taxonomy level reports output by Metaphlan2Classifier: Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.
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
This BioModule will merge forward and reverse fastq files using PEAR.
For more informations, see the online PEAR manual: https://sco.h-its.org/exelixis/web/software/pear/doc.html
PearMergeReads() - Constructor for class biolockj.module.seq.PearMergeReads
 
PHYLUM - Static variable in class biolockj.Constants
Config option for "report.taxonomyLevels": "phylum"
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.
BioModules 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
Config option for property: "pipeline.env"
Used to indicate running as an Amazon web service: "aws"
PIPELINE_ENV_CLUSTER - Static variable in class biolockj.Constants
Config option for property: "pipeline.env"
Used to indicate running on the cluster: "cluster"
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
Config List property: "pipeline.env"
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
Internal Config String property: "taxa_count_log_norm"
Set as the value of "internal.pipelineInputTypes" for log-normalized taxa count files that meet the file requirements to pass TaxaUtil.isLogNormalizedTaxaFile(File).
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
Internal Config String property: "taxa_count_norm"
Set as the value of "internal.pipelineInputTypes" for normalized taxa count files that meet the file requirements to pass TaxaUtil.isNormalizedTaxaFile(File).
PIPELINE_OTU_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
Internal Config String property: "otu_count"
Set as the value of "internal.pipelineInputTypes" for OTU count files that meet the file requirements to pass OtuUtil.isOtuFile(File).
PIPELINE_PAIRED_READS_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
Internal Config String property: "paired"
Set as the value of "internal.pipelineInputTypes" for paired sequence input files.
PIPELINE_PARSER_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
Internal Config String property: "classifier_output"
Set as the value of "internal.pipelineInputTypes" for classifier output files.
PIPELINE_PRIVS - Static variable in class biolockj.Constants
Config property: "pipeline.permissions"
PIPELINE_R_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
Internal Config String property: "R"
Set as the value of "internal.pipelineInputTypes" if input files are some type of count table merged with the metadata such as those output by AddMetadataToTaxaTables.
PIPELINE_SEQ_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
Internal Config String property: "seq"
Set as the value of "internal.pipelineInputTypes" for sequence input files.
PIPELINE_STATS_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
Internal Config String property: "stats"
Set as the value of "internal.pipelineInputTypes" if input files are tables of statistics such as those output by R_CalculateStats.
PIPELINE_STATUS - Static variable in class biolockj.util.SummaryUtil
 
PIPELINE_TAXA_COUNT_TABLE_INPUT_TYPE - Static variable in class biolockj.util.BioLockJUtil
Internal Config String property: "taxa_count"
Set as the value of "internal.pipelineInputTypes" for taxa count files that meet the file requirements to pass TaxaUtil.isTaxaFile(File).
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
ScriptModules that generate scripts will submit a main script to the OS for execution as a Processor.
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
Constructor called when "pipeline.defaultProps" contains a valid file-path
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.
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