A B C D E F G H I J K L M N O P Q R S T U V W

I

ignoreFile(File) - Static method in class biolockj.util.BioLockJUtil

Method used to add a file to the ignore file list property.

ILLUMINA_FW_READ_IND - Static variable in class biolockj.util.SeqUtil

Illumina forward read indicator found in sequence header

ILLUMINA_RV_READ_IND - Static variable in class biolockj.util.SeqUtil

Illumina reverse read indicator found in sequence header

ImportMetadata - Class in biolockj.module.implicit

This BioModule validates the contents/format of the project metadata file and the related Config properties.

ImportMetadata() - Constructor for class biolockj.module.implicit.ImportMetadata

inAwsEnv() - Static method in class biolockj.util.DockerUtil

Return TRUE if running in AWS (based on Config props).

INDENT - Static variable in class biolockj.Constants

Standard indent = 4 spaces.

inDockerEnv() - Static method in class biolockj.util.DockerUtil

Return TRUE if running in AWS (based on Config props).

INFO - Static variable in class biolockj.Log

INFO log message type

info(Class<?>, String) - Static method in class biolockj.Log

Print log level INFO message.

init() - Method in interface biolockj.module.BioModule

Initialize a new module to generate a unique ID and module directory.

init() - Method in class biolockj.module.BioModuleImpl

This method must be called immediately upon instantiation.

initBioLockJ(String[]) - Static method in class biolockj.BioLockJ

Execution summary:
Call MemoryUtil.reportMemoryUsage(String) for baseline memory info Call registerRuntimeParameters(String[]) Call MetaUtil.initialize() to verify metadata dependencies Call Config.initialize() to create pipeline root dir and load properties Initialize Log with /resources/log4J.properties Copy initial metadata file into the pipeline root directory Call SeqUtil.initialize() to set Config parameters based on sequence files

initialize() - Static method in class biolockj.Config

Initialize Config by reading in properties from config runtime parameter.

initialize(String) - Static method in class biolockj.Log

Called by BioLockJ.main() after Config is initialized.

initialize() - Static method in class biolockj.util.MetaUtil

Check dependencies used to handle the metadata file are defined and unique.

initialize() - Static method in class biolockj.util.SeqUtil

Initialize Config params set by SeqUtil.

initializeMaps() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser

Sample IDs in the original metadata file may contain restricted characters that will be replaced with a "." via {link biolockj.module.implicit.qiime.BuildQiimeMapping}.

initializeModules() - Static method in class biolockj.Pipeline

Initialization occurs by calling BioModule methods on configured modules
Create module sub-directories under "internal.pipelineDir" as ordered in Config file.
Reset the SummaryUtil module so previous summary descriptions can be used for completed modules Delete incomplete module contents if restarting a failed pipeline "output" directory
Call Pipeline.refreshOutputMetadata(BioModule) to cache metadata if output by a complete module
Call Pipeline.refreshRCacheIfNeeded(BioModule) to cache R fields after 1st R module runs
Verify dependencies with BioModule.checkDependencies()

initializePipeline() - Static method in class biolockj.Pipeline

This method initializes the Pipeline by building the modules and checking module dependencies.

initMainScript(ScriptModule) - Static method in class biolockj.util.BashScriptBuilder

Create the ScriptModule main script that calls all worker scripts.

initRestart() - Static method in class biolockj.BioLockJ

Initialize restarted pipeline by: Initialize Log file using the name of the pipeline root directory Update summary #Attempts count Delete status file "biolockjFailed" in pipeline root directory If pipeline status = "biolockjComplete" Delete file "downloadList.txt" in pipeline root directory

initSeqParams() - Static method in class biolockj.util.SeqUtil

Set "input.ignoreFiles", , and Ignore the metadata file Config."metadata.filePath" If Config pipeline contains biolockj.module.seq or biolockj.module.classifier BioModules, ignore non-(fasta/fastq) files found in Constants.INPUT_DIRS

initTaxaLevels() - Static method in class biolockj.util.TaxaUtil

Set taxonomy levels ordered by level, from highest to lowest.

initWorkerScript(ScriptModule, String) - Static method in class biolockj.util.BashScriptBuilder

Create the numbered worker scripts.

INPUT_DIR_FLAG - Static variable in class biolockj.util.RuntimeParamUtil

Input directory file-path runtime parameter switch: "i"

INPUT_DIRS - Static variable in class biolockj.Constants

Config List property: "input.dirPaths"
Set sequence file directories

INPUT_FORWARD_READ_SUFFIX - Static variable in class biolockj.Constants

Config String property: "input.suffixFw"
Set file suffix used to identify forward reads in "input.dirPaths"

INPUT_IGNORE_FILES - Static variable in class biolockj.Constants

Config List property: "input.ignoreFiles"
Set file names to ignore if found in "input.dirPaths"

INPUT_RAREFYING_MAX - Static variable in class biolockj.module.seq.RarefySeqs

Config property "rarefySeqs.max" defines the maximum number of reads per file

INPUT_RAREFYING_MIN - Static variable in class biolockj.module.seq.RarefySeqs

Config property "rarefySeqs.min" defines the minimum number of reads per file

INPUT_REQUIRE_COMPLETE_PAIRS - Static variable in class biolockj.Constants

Config Boolean property: "input.requireCompletePairs"
Require 100% sequence input files are matching paired reads

INPUT_REQUIRE_PRIMER - Static variable in class biolockj.module.seq.TrimPrimers

Config property "trimPrimers.requirePrimer" is a boolean used to determine if sequences without a primer should be kept or discarded

INPUT_REVERSE_READ_SUFFIX - Static variable in class biolockj.Constants

Config String property: "input.suffixRv"
Set file suffix used to identify forward reads in "input.dirPaths"

INPUT_SEQ_MAX - Static variable in class biolockj.module.seq.SeqFileValidator

Config Integer property "seqFileValidator.seqMaxLen" defines the maximum number of bases per read

INPUT_SEQ_MIN - Static variable in class biolockj.module.seq.SeqFileValidator

Config Integer property "seqFileValidator.seqMinLen" defines the minimum number of bases per read

INPUT_TRIM_PREFIX - Static variable in class biolockj.Constants

Config String property: "input.trimPrefix"
Set value of prefix to trim from sequence file names or headers to obtain Sample ID.

INPUT_TRIM_SEQ_FILE - Static variable in class biolockj.Constants

Config property "trimPrimers.filePath" defines the file path to the file that defines the primers as regular expressions.

INPUT_TRIM_SUFFIX - Static variable in class biolockj.Constants

Config String property: "input.trimSuffix"
Set value of suffix to trim from sequence file names or headers to obtain Sample ID.

inQuotes(String) - Method in class biolockj.module.implicit.ImportMetadata

Method called each time a line from metadata contains the Config."metadata.columnDelim".

INTERNAL_ALL_MODULES - Static variable in class biolockj.Constants

Internal Config List property: "internal.allModules"
List of all configured, implicit, and pre/post-requisite modules for the pipeline.
Example: biolockj.module.ImportMetadata, etc.

INTERNAL_BLJ_MODULE - Static variable in class biolockj.Constants

Internal Config List property: "internal.configModules"
List of all project config modules.

INTERNAL_DEFAULT_CONFIG - Static variable in class biolockj.Constants

Internal Config List property: "internal.defaultConfig"
List of all nested default config files.

INTERNAL_IS_MULTI_LINE_SEQ - Static variable in class biolockj.Constants

Config Internal Boolean property: "internal.isMultiLineSeq"
Store TRUE if SeqUtil determines input sequences are multi-line format.

INTERNAL_MULTIPLEXED - Static variable in class biolockj.Constants

Config Boolean property: "internal.multiplexed"
Set to true if multiplexed reads are found, set by the application runtime code.

INTERNAL_PAIRED_READS - Static variable in class biolockj.Constants

Config Boolean property: "internal.pairedReads"
Set to true if paired reads are found, set by the application runtime code.

INTERNAL_PIPELINE_DIR - Static variable in class biolockj.Constants

Config String property: "internal.pipelineDir"
Stores the path of the pipeline root directory path set by the application runtime code.

INTERNAL_PIPELINE_INPUT_TYPES - Static variable in class biolockj.util.BioLockJUtil

Internal Config String property: "internal.pipelineInputTypes"
This value is set after parsing the input files from Config property: "input.dirPaths" in the method: BioLockJUtil.getPipelineInputFiles().

INTERNAL_SEQ_HEADER_CHAR - Static variable in class biolockj.Constants

Config property: "internal.seqHeaderChar"
The property holds the 1st character used in the sequence header for the given dataset

INTERNAL_SEQ_TYPE - Static variable in class biolockj.Constants

Config Internal property: "internal.seqType"
The sequence type requires either "fasta" or "fastq"
System will auto-detect if not configured

isComplete(BioModule) - Static method in class biolockj.util.ModuleUtil

Return TRUE if module completed successfully.

isDirectMode() - Static method in class biolockj.util.DockerUtil

Return TRUE if runtime parameters indicate attempt to run in direct mode

isDockerMode() - Static method in class biolockj.util.RuntimeParamUtil

Return TRUE if runtime parameter "-docker" was found

isFastA() - Static method in class biolockj.util.SeqUtil

Return TRUE if input files are in FastA format.

isFastQ() - Static method in class biolockj.util.SeqUtil

Return TRUE if input files are in FastQ format.

isFirstRModule(BioModule) - Static method in class biolockj.util.ModuleUtil

Test if module is the first R_Module configured in the pipeline.

isForwardRead(String) - Static method in class biolockj.util.SeqUtil

Return TRUE if reads are unpaired or if name does not contain the reverse read file suffix:

isGzipped(String) - Static method in class biolockj.util.SeqUtil

Determine if file is gzipped based on its file extension.
Any file ending with ".gz" is treated as a gzipped file.

isHumann2CountModule(BioModule) - Method in class biolockj.module.report.humann2.Humann2CountModule

Check the module to determine if it generated OTU count files.

isIncomplete(BioModule) - Static method in class biolockj.util.ModuleUtil

Return TRUE if module started execution but is not complete.

isLogNormalizedTaxaFile(File) - Static method in class biolockj.util.TaxaUtil

Check the file name to determine if it is a Log normalized taxonomy table file.

isMetadataModule(BioModule) - Static method in class biolockj.util.ModuleUtil

Method determines if the given module is a metadata-module (which does not use/modify sequence data.

isMetaMergeTable(File) - Static method in class biolockj.util.RMetaUtil

Method analyzes the file name to determine if the file could be output from the BioModule AddMetadataToTaxaTables

isMultiplexed() - Static method in class biolockj.util.SeqUtil

Check current state of sequence data.

isNormalizedTaxaFile(File) - Static method in class biolockj.util.TaxaUtil

Check the file name to determine if it is a normalized taxonomy table file.

isOnCluster() - Static method in class biolockj.Config

Check if running on cluster

isOtuFile(File) - Static method in class biolockj.util.OtuUtil

Check the file name and contents to determine if file is an OTU count file.

isOtuModule(BioModule) - Method in class biolockj.module.report.otu.OtuCountModule

Check the module to determine if it generated OTU count files.

isPathwayFile(File) - Static method in class biolockj.util.PathwayUtil

Check the file name to determine if it is a pathway abundance table file.

isPathwayModule(BioModule) - Static method in class biolockj.util.PathwayUtil

Check the module to determine if it generated OTU count files.

isPipelineComplete() - Static method in class biolockj.BioLockJ

Determine project status based on existence of "biolockjComplete" in pipeline root directory.

isSeqFile(File) - Static method in class biolockj.util.SeqUtil

Verify 1st character of sequence header and mask 1st sequence for valid DNA/RNA bases "acgtu"

isSeqModule(BioModule) - Static method in class biolockj.util.SeqUtil

Check the module to determine if it generated sequence file output.

isStatsFile(File) - Static method in class biolockj.module.report.r.R_CalculateStats

Analyze file name for key strings to determine if file is a stats file output by this module.

isTaxaFile(File) - Static method in class biolockj.util.TaxaUtil

Check the file name to determine if it is a taxonomy table file.

isTaxaModule(BioModule) - Method in class biolockj.module.report.taxa.TaxaCountModule

Check the module output directory for taxonomy table files generated by BioLockJ.

isValid(OtuNode) - Method in class biolockj.module.implicit.parser.ParserModuleImpl

Some ClassifierModules can include taxonomy level identifiers without an OTU name in the sample report files.

isValid(OtuNode) - Method in class biolockj.module.implicit.parser.r16s.RdpParser

If RdpNode.getScore() is above the Config., continue with the standard OtuNode validation.

isValidInputModule(BioModule) - Method in interface biolockj.module.BioModule

BioModules BioModule.getInputFiles() method typically, but not always, return the previousModule output files.

isValidInputModule(BioModule) - Method in class biolockj.module.BioModuleImpl

In the early stages of the pipeline, starting with the very 1st module ImportMetadata, most modules expect sequence files as input.

isValidInputModule(BioModule) - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser

isValidInputModule(BioModule) - Method in class biolockj.module.implicit.qiime.QiimeClassifier

If superclass is fed by another QiimeClassifier, it must be a subclass with biom output.

isValidInputModule(BioModule) - Method in class biolockj.module.JavaModuleImpl

If module is a SeqModule input must contain sequence data.

isValidInputModule(BioModule) - Method in class biolockj.module.report.humann2.Humann2CountModule

isValidInputModule(BioModule) - Method in class biolockj.module.report.JsonReport

isValidInputModule(BioModule) - Method in class biolockj.module.report.otu.OtuCountModule

isValidInputModule(BioModule) - Method in class biolockj.module.report.taxa.TaxaCountModule

isValidInputModule(BioModule) - Method in class biolockj.module.SeqModuleImpl

A B C D E F G H I J K L M N O P Q R S T U V W