- 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
-
Check runtime env for /.dockerenv
- 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
-
- initDir - Variable in class biolockj.launch.LaunchProcess
-
- 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
-
- initialize() - Static method in class biolockj.util.MetaUtil
-
Check required properties 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}.
- 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.
- initPipelineInput() - Static method in class biolockj.util.BioLockJUtil
-
Basic input files may be sequences, or any other file type acceptable in a pipeline module.
- 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
-
- 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_ALLOW_DUPS - Static variable in class biolockj.Constants
-
- INPUT_DIRS - Static variable in class biolockj.Constants
-
Config
List property: "input.dirPaths"
- INPUT_FORWARD_READ_SUFFIX - Static variable in class biolockj.Constants
-
- INPUT_IGNORE_FILES - Static variable in class biolockj.Constants
-
Config
List property: "input.ignoreFiles"
- 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
-
- INPUT_REQUIRE_COMPLETE_PAIRS_DESC - Static variable in class biolockj.Constants
-
- 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
-
- 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"
- INPUT_TRIM_SEQ_FILE - Static variable in class biolockj.module.seq.TrimPrimers
-
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"
- INPUT_TYPES - Static variable in class biolockj.Constants
-
Config
List property: "pipeline.inputTypes"
- InputDataModule - Interface in biolockj.module.getData
-
This interface identifies modules that retrieve data.
- inQuotes(String) - Method in class biolockj.module.implicit.ImportMetadata
-
- insertPathVars(ScriptModule, List<String>) - Static method in class biolockj.util.BashScriptBuilder
-
Paths to common module directories are added via pathVariableVals
.
- INTEGER_TYPE - Static variable in class biolockj.Properties
-
- IntentionalStop - Exception in biolockj.exception
-
Parent exception for BioLockJ Exception that arise when the user explicitly intended to make the pipeline stop.
- IntentionalStop(String) - Constructor for exception biolockj.exception.IntentionalStop
-
- 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_ID - Static variable in class biolockj.Constants
-
Config
String property: "internal.pipelineInstanceId"
The pipeline instance id is generally formed from the pipeline name,
the date the pipeline started and sometimes an additional integer to ensure an unique folder name.
- INTERNAL_PIPELINE_INPUT_TYPES - Static variable in class biolockj.util.BioLockJUtil
-
- INTERNAL_PIPELINE_NAME - Static variable in class biolockj.Constants
-
Config
String property: "internal.pipelineName"
Stores the name of the pipeline.
- INTERNAL_PREFIX - Static variable in class biolockj.Constants
-
Any
Config
property that starts with the "internal."
prefix will not be included in the final MASTER properties file.
- 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
- InterruptTimerTask(Thread) - Constructor for class biolockj.launch.JavaLaunchProcess.InterruptTimerTask
-
- inTestMode() - Static method in class biolockj.launch.LaunchProcess
-
- InvalidPipelineException - Exception in biolockj.exception
-
- InvalidPipelineException(String) - Constructor for exception biolockj.exception.InvalidPipelineException
-
- InvalidPipelineException(File) - Constructor for exception biolockj.exception.InvalidPipelineException
-
- isAwsMode() - Static method in class biolockj.util.RuntimeParamUtil
-
Return TRUE if runtime parameter
"-aws" was found
- isComplete(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Return TRUE if module completed successfully.
- isDeprecatedProp(String) - Static method in class biolockj.Properties
-
Determines if the given prop is in the list of deprecated properties.
- isDirectMode() - Static method in class biolockj.util.BioLockJUtil
-
Return TRUE if runtime parameters indicate attempt to run in direct mode
- 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.
- isInDocker() - Static method in class biolockj.util.RuntimeParamUtil
-
- isInternalProperty(String) - Static method in class biolockj.Config
-
- isLocalImage(BioModule, String) - Static method in class biolockj.util.DockerUtil
-
- 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
-
- isModuleDir(File) - Method in interface biolockj.pipelines.OtherPipeline
-
- isModuleDir(File) - Method in class biolockj.pipelines.OtherPipelineImpl
-
- isModuleDir(File) - Static method in class biolockj.pipelines.PipelineUtil
-
Determine if a given directory is a module directory in a pipeline.
- 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.
- isParentDir(String, String) - Method in class biolockj.util.paths.BasicDockerMapper
-
- 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.
- isPipelineDir(File) - Static method in class biolockj.pipelines.PipelineUtil
-
Determine if a given directory is a valid pipeline.
- isPrecheckAllMode() - Static method in class biolockj.util.RuntimeParamUtil
-
- isPrecheckMode() - Static method in class biolockj.util.RuntimeParamUtil
-
- isPrecheckPipeline() - Method in interface biolockj.pipelines.OtherPipeline
-
Determine if a given pipeline was run in precheck mode, ie using the
parameter.
- isPrecheckPipeline() - Method in class biolockj.pipelines.OtherPipelineImpl
-
- isPrecheckPipeline(File) - Static method in class biolockj.pipelines.PipelineUtil
-
Determine if a given pipeline was run in precheck mode, ie using the parameter.
- isReplacementForPrecheck() - Method in class biolockj.launch.LaunchProcess
-
- 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
ClassifierModule
s 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
-
- isValidExeProp(BioModule, String) - Static method in class biolockj.Properties
-
Verify that a given exe property has a valid value.
- isValidInputModule(BioModule) - Method in interface biolockj.module.BioModule
-
- 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.diversity.ShannonDiversity
-
- isValidInputModule(BioModule) - Method in class biolockj.module.hello_world.Step4
-
- isValidInputModule(BioModule) - Method in class biolockj.module.implicit.parser.r16s.RdpHierParser
-
- isValidInputModule(BioModule) - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser
-
- isValidInputModule(BioModule) - Method in class biolockj.module.implicit.qiime.MergeQiimeOtuTables
-
- 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.rnaseq.DESeq2
-
DESeq should only take raw values.
- isValidInputModule(BioModule) - Method in class biolockj.module.rnaseq.EdgeR
-
edgeR should only take raw values.
- isValidInputModule(BioModule) - Method in class biolockj.module.SeqModuleImpl
-
- isValidProp(String) - Method in interface biolockj.api.ApiModule
-
Tests to see if the value val is valid for property prop; primarily tests format.
- isValidProp(String, String, List<String>) - Static method in class biolockj.api.BioLockJ_API
-
Returns true if the
- isValidProp(String) - Method in class biolockj.module.BioModuleImpl
-
- isValidProp(String) - Method in class biolockj.module.classifier.wgs.Humann2Classifier
-
- isValidProp(String) - Method in class biolockj.module.diy.GenMod
-
- isValidProp(String) - Method in class biolockj.module.diy.Rmarkdown
-
- isValidProp(String) - Method in class biolockj.module.getData.sra.SequenceReadArchive
-
- isValidProp(String) - Method in class biolockj.module.getData.sra.SraDownload
-
- isValidProp(String) - Method in class biolockj.module.getData.sra.SraMetaDB
-
- isValidProp(String) - Method in class biolockj.module.hello_world.Hello_Friends
-
- isValidProp(String) - Method in class biolockj.module.hello_world.Step3
-
- isValidProp(String) - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser
-
- isValidProp(String) - Method in class biolockj.module.report.otu.RemoveLowOtuCounts
-
- isValidProp(String) - Method in class biolockj.module.report.taxa.LogTransformTaxaTables
-
- isValidProp(String) - Method in class biolockj.module.rnaseq.DESeq2
-
- isValidProp(String) - Method in class biolockj.module.rnaseq.EdgeR
-
- isValidProp(String) - Method in class biolockj.module.ScriptModuleImpl
-
- isValidProp(String) - Method in class biolockj.module.seq.KneadData
-
- isValidProp(String) - Method in class biolockj.module.seq.SeqFileValidator
-
- isValidProp(String) - Static method in class biolockj.Properties
-
Check if a property has a value in a valid format.
- isVerbose() - Static method in class biolockj.util.RuntimeParamUtil
-
- isWindowsHostPath(String) - Method in class biolockj.util.paths.CommonDockerMapper
-