G-Index

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

G

generateMergedTables() - Method in class biolockj.module.report.humann2.AddMetadataToPathwayTables: Create the merged metadata tables.
generateMergedTables() - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables: Create the merged metadata tables.
generateOtuput(File, TreeMap<String, Long>) - Static method in class biolockj.module.report.otu.RarefyOtuCounts: Print the output file wit rarefied counts.
GENUS - Static variable in class biolockj.Constants: Config option for "report.taxonomyLevels": "genus"
GENUS_DELIM - Static variable in class biolockj.node.OtuNodeImpl: Standard classifier output level delimiter for GENUS
getAdminEmailPassword() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for "p"
getBaseDir() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for "b"
getBaseDirParam() - Static method in class biolockj.util.RuntimeParamUtil: Get the baseDir param and value
getBashVar(String) - Static method in class biolockj.Processor: Return the value of the bash variable from the runtime shell.
getBatch(List<String>, int, int) - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier: Method returns batch script lines for one batch.
getBatchDir(int) - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier: Get the pipeline/module/temp/batch_# dir.
getBatchFastaDir(int) - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier: Get the pipeline/module/temp/batch_#/fasta directory.
getBinaryFields(BioModule) - Static method in class biolockj.util.RMetaUtil: Get the Config."R_internal.binaryFields" fields containing only 2 non-numeric values.
getBljDir() - Static method in class biolockj.util.BioLockJUtil: Get the program source (either the jar path or main class biolockj.BioLockJ);
getBoolean(BioModule, String) - Static method in class biolockj.Config: Parse property value (Y or N) to return boolean, if not found, return false;
getClassifier(BioModule, boolean) - Static method in class biolockj.util.ModuleUtil: Get a classifier module
Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
getClassifierExe() - Method in interface biolockj.module.classifier.ClassifierModule: Get the executable required to classify your samples.
getClassifierExe() - Method in class biolockj.module.classifier.ClassifierModuleImpl
getClassifierExe() - Method in class biolockj.module.classifier.r16s.RdpClassifier: RDP uses java to run a JAR file, so no special command is required
getClassifierExe() - Method in class biolockj.module.classifier.wgs.Humann2Classifier: Get kraken executable command: "exe.humann2"
getClassifierExe() - Method in class biolockj.module.classifier.wgs.Kraken2Classifier: Get kraken executable command: "exe.kraken2"
getClassifierExe() - Method in class biolockj.module.classifier.wgs.KrakenClassifier: Get kraken executable command: "exe.kraken"
getClassifierExe() - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier: Metaphlan runs python scripts, so no special command is required
getClassifierExe() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: QIIME calls python scripts, so no special command is required
getClassifierParams() - Method in interface biolockj.module.classifier.ClassifierModule: Get optional list of parameters to append whenever the classifier executable is called.
getClassifierParams() - Method in class biolockj.module.classifier.ClassifierModuleImpl
getClassifierParams() - Method in class biolockj.module.classifier.r16s.RdpClassifier: Do not accept -t to define a database, since that instead requires the specific property: "rdp.db"
getClassifierParams() - Method in class biolockj.module.classifier.wgs.Humann2Classifier: Obtain the humann2 runtime params
getClassifierParams() - Method in class biolockj.module.classifier.wgs.Kraken2Classifier: Obtain the kraken2 runtime params
getClassifierParams() - Method in class biolockj.module.classifier.wgs.KrakenClassifier: Obtain the kraken runtime params
getClassifierParams() - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier: Obtain the metaphlan2 runtime params
getClassifierParams() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: Obtain the QIIME runtime params
getClassifierType() - Method in class biolockj.module.classifier.ClassifierModuleImpl: This method returns the classifier class name in lower case, after "classifier" is removed.
The remaining text should uniquely identify the name of the program.
The basic deployment will return one of: (rdp, qiime, kraken, metaphlan2, or humann2).
getClassNames(Collection<?>) - Static method in class biolockj.util.BioLockJUtil: Return an ordered list of the class names from the input collection.
getClusterUser() - Static method in class biolockj.util.DownloadUtil: If System.user.home is a file path (like /usr/home/johnDoe), return last directory name (johnDoe).
getCollectionAsString(Collection<?>) - Static method in class biolockj.util.BioLockJUtil: Concatenate data and return as a comma separated String.
getCommonParent(File, File) - Static method in class biolockj.util.BioLockJUtil: Compare files to return a common parent directory (if any)
getConfigFile() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for "c"
getConfigFileExt() - Static method in class biolockj.Config: Gets the configuration file extension (often ".properties")
getConfigFileName() - Static method in class biolockj.Config: Gets the configuration file name
getConfigFileParam() - Static method in class biolockj.util.RuntimeParamUtil: Used to build Docker run commands.
getConfigFilePath() - Static method in class biolockj.Config: Gets the full Config file path passed to BioLockJ as a runtime parameter.
getCount() - Method in class biolockj.node.JsonNode: Getter method for count
getCount() - Method in interface biolockj.node.OtuNode: Gets the OTU count.
getCount() - Method in class biolockj.node.OtuNodeImpl
getCount() - Method in class biolockj.util.OtuUtil.OtuCountLine: Get OTU count
getCountSummary(Map<String, String>, String, boolean) - Static method in class biolockj.util.SummaryUtil: Return the min/max/mean/median summary stats for the given metadata numeric column
getData(String, TreeMap<String, Long>) - Static method in class biolockj.module.report.otu.RarefyOtuCounts: Get OTU count data for the given sampleId.
getDB() - Method in class biolockj.module.classifier.ClassifierModuleImpl
getDB() - Method in class biolockj.module.classifier.r16s.RdpClassifier
getDB() - Method in class biolockj.module.classifier.wgs.Humann2Classifier
getDB() - Method in class biolockj.module.classifier.wgs.Kraken2Classifier
getDB() - Method in class biolockj.module.classifier.wgs.KrakenClassifier
getDB() - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier
getDB() - Method in interface biolockj.module.DatabaseModule: Return database directory, if multiple databases are configured, they must share a common parent directory and the common parent directory is returned by this method.
getDB() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: Check DB parameters for the comment parent directory path, there are 3 parameters: "qiime.pynastAlignDB" "qiime.refSeqDB" "qiime.taxaDB"
getDB() - Method in class biolockj.module.seq.KneadData
getDBs() - Method in class biolockj.module.seq.KneadData: Get the configured database parameters
getDefaultConfig(File) - Static method in class biolockj.Properties: Parse property file for the property "pipeline.defaultProps".
getDefaultDemultiplexer() - Static method in class biolockj.util.ModuleUtil: Get the Java Class name for the default Demultiplexer module
getDefaultFastaConverter() - Static method in class biolockj.util.ModuleUtil: Get the Java Class name for the default Fasta converter module
getDefaultMergePairedReadsConverter() - Static method in class biolockj.util.ModuleUtil: Get the Java Class name for the default Merge paired read module
getDefaultStatsModule() - Static method in class biolockj.util.ModuleUtil: Return the class name of the default R statistics BioModule
getDepricatedOtuCountFields() - Static method in class biolockj.module.implicit.parser.ParserModuleImpl: Getter for depricatedOtuCountFields
getDepricatedReadFields() - Static method in class biolockj.module.implicit.RegisterNumReads: Getter for depricatedReadFields
getDirectModuleDir() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for "d"
getDirectModuleParam(BioModule) - Static method in class biolockj.util.RuntimeParamUtil: Direct module parameters contain 2 parts separated by a colon: (pipeline directory name):(module name)
getDirectPipelineDir() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for direct module pipeline directory
getDirFilter(boolean, boolean, boolean) - Static method in class biolockj.util.DownloadUtil: Get a directory name filter to include module sub-directories.
getDockerDB(String) - Method in class biolockj.module.implicit.qiime.QiimeClassifier: Return the Docker container database directory (starting with /db/...)
getDockerHostBLJ() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for Docker host BioLockJ dir
getDockerHostBLJ_SUP() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for Docker host blj_support dir
getDockerHostConfigDir() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for "C"
getDockerHostHomeUserDir() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for Docker host $USER $HOME dir
getDockerHostInputDir() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for "i"
getDockerHostMetaDir() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for "m"
getDockerHostPipelineDir() - Static method in class biolockj.util.RuntimeParamUtil: Runtime property getter for Docker host pipeline dir
getDockerImage(BioModule) - Static method in class biolockj.util.DockerUtil: Return the name of the Docker image needed for the given module.
getDockerJavaModuleParams() - Static method in class biolockj.util.RuntimeParamUtil: Get Docker runtime arguments passed to BioLockJ from dockblj script.
These are used to to populate BLJ_OPTIONS in Docker java_module scripts.
getDockerUser(BioModule) - Static method in class biolockj.util.DockerUtil: Return the Docker Hub user ID.
getDockerVolumeDir(String, String) - Static method in class biolockj.util.DockerUtil: Get mapped Docker system File from Config directory-property by replacing the host system path with the mapped container path.
getDockerVolumeFile(String, String) - Static method in class biolockj.util.DockerUtil: Get mapped Docker system File from Config file-property by replacing the host system path with the mapped container path.
getDockerVolumePath(String, String) - Static method in class biolockj.util.DockerUtil: Get Docker file path through mapped volume
getDoubleVal(BioModule, String) - Static method in class biolockj.Config: Parse property for numeric (double) value
getDownloadCmd() - Static method in class biolockj.util.DownloadUtil: If running on cluster, build command for user to download pipeline analysis.
getDownloadDirPath() - Static method in class biolockj.util.DownloadUtil: Get validated Config."pipeline.downloadDir" if running on cluster, otherwise return null
getDownloadListFile() - Static method in class biolockj.util.DownloadUtil: Get the download list file.
getDownloadModules() - Static method in class biolockj.util.DownloadUtil: Get the modules to download.
getDownloadSize(List<File>) - Static method in class biolockj.util.DownloadUtil: Get the total size of all files included for download.
getExe(BioModule, String) - Static method in class biolockj.Config: Get exe.* property name.
getExeParams(BioModule, String) - Static method in class biolockj.Config: Call this function to get the parameters configured for this property.
Make sure the last character for non-null results is an empty character for use in bash scripts calling the corresponding executable.
getExistingDir(BioModule, String) - Static method in class biolockj.Config: Get a valid File directory or return null
getExistingFile(BioModule, String) - Static method in class biolockj.Config: Get a valid File or return null.
getExistingFileObject(String) - Static method in class biolockj.Config: Build File using filePath.
getField(String, String) - Static method in class biolockj.util.MetaUtil: Get metadata field value for given sampleId.
getFieldNames() - Static method in class biolockj.util.MetaUtil: Get a list of all metadata fields (metadata file column names except the 1st).
getFieldValues(String, boolean) - Static method in class biolockj.util.MetaUtil: Get metadata column for given field name.
getFile() - Static method in class biolockj.Log: Returns the log file.
getFileCache() - Method in class biolockj.module.BioModuleImpl: Get cached input files
getFileName() - Static method in class biolockj.util.MetaUtil: Get the metadata file name, if it exists, otherwise return projectName.tsv
getFileNameColumn(String) - Method in class biolockj.module.implicit.parser.r16s.QiimeParser: Examines the header line to find the column index for "BioLockJFileName" which holds the demultiplexed sample file name.
getFilePaths(Collection<File>) - Static method in class biolockj.util.BioLockJUtil: Return an ordered list of absolute file paths from the input collection.
getFileReader(File) - Static method in class biolockj.util.BioLockJUtil: Get a BufferedReader for standard text file or GZIPInputStream for gzipped files ending in ".gz"
getFooter() - Static method in class biolockj.util.SummaryUtil: Print the final lines of the summary with overall status, runtime, and the download scp command if applicable.
getForcedColumnName(String) - Static method in class biolockj.util.MetaUtil: Used to generate a guaranteed to be unique column name.
getHeader(File, List<String>) - Method in class biolockj.module.seq.Multiplexer: Get the header for the sequence.
getHeader(String) - Static method in class biolockj.util.SeqUtil: Extract the header from the first line of a read (parse to first space).
getHeaders(File) - Static method in class biolockj.util.SeqUtil: Return the header of each read in the sequence file.
getHeaders(File, File) - Static method in class biolockj.util.SeqUtil: Get valid headers found in both forward and reverse read.
getHelpInfo(File) - Static method in class biolockj.BioLockJ: Print error file path, restart instructions, and link to the BioLockJ Wiki
getHn2ClassifierOutput(String) - Static method in class biolockj.util.PathwayUtil: Humann2 classifier outputs 3 types of files: "pAbund" "pCovg" "geneFam" Given the type, this method retuns the output file name.
getHn2Type(File) - Static method in class biolockj.util.PathwayUtil: Humann2 classifier outputs 3 types of files: "pAbund" "pCovg" "geneFam" This method returns the type included in the given file name.
getID() - Method in interface biolockj.module.BioModule: Some BioModules may be added to a pipeline multiple times so must be identified by an ID.
This is the same value as the directory folder prefix when run.
The 1st module ID is 0 (or 00 if there are more than 10 modules.
getID() - Method in class biolockj.module.BioModuleImpl
getID() - Static method in class biolockj.util.MetaUtil: Get the metadata file ID column name.
getIdMap() - Static method in class biolockj.util.DemuxUtil: Return the ID map (key=barcodeID, value=sampleId) Print the map to the log file.
Barcodes, if used, are located in the metadata column defined by property: Config."metadata.barcodeColumn"
getImageName(BioModule) - Static method in class biolockj.util.DockerUtil: Return the Docker Image name for the given class name.
Return "blj_bash" for simple bash script modules that don't rely on special software
Class names contain no spaces, words are separated via CamelCaseConvension.
Docker image names cannot contain upper case letters, so this method substitutes "_" before the lower-case version of each capital letter.

Example: JavaModule becomes java_module
getImageVersion(BioModule) - Static method in class biolockj.util.DockerUtil: Get the Docker image version if defined in the Config file
If not found, return the default version "latest"
getInitialProperties() - Static method in class biolockj.Config: Get initial properties ordered by property
getInputDirs() - Static method in class biolockj.util.BioLockJUtil: Get the list of input directories for the pipeline.
getInputFileDir() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: Module input directories are set to the previous module output directory.
To ensure we use the correct path, get path from QiimeClassifier.getInputFiles()
getInputFiles() - Method in interface biolockj.module.BioModule: Each BioModule takes the previous BioModule output as input:
BioModule[ n ].getInputFiles() = BioModule[ n - 1 ].getOutputDir().listFiles()
Special cases:
The 1st BioModule return all files in "input.dirPaths"
If previous BioModule BioModule[ n - 1 ] is a MetadataModule, forward it's input + output file: BioModule[ n ].getInputFiles() = BioModule[ n -1 ].getInputFiles() + BioModule[ n -1 ].getOutputFiles()
getInputFiles() - Method in class biolockj.module.BioModuleImpl: BioModule BioModuleImpl.getInputFiles() is called to initialize upon first call and cached.
getInputFiles() - Method in class biolockj.module.implicit.parser.r16s.QiimeParser: Get only the lowest level report since it contains taxa info for all higher OTU reports.
getInputFiles() - Method in class biolockj.module.implicit.qiime.QiimeClassifier
getInputFiles() - Method in class biolockj.module.report.humann2.Humann2CountModule
getInputFiles() - Method in class biolockj.module.report.otu.OtuCountModule
getInputFiles() - Method in class biolockj.module.report.taxa.TaxaCountModule
getInputFiles() - Method in class biolockj.module.SeqModuleImpl: Return SeqModuleImpl.getSeqFiles(Collection) to filter standard module input files.
getInputSummary(BioModule) - Static method in class biolockj.util.SummaryUtil: Build a summary of the input files for the given module
getIupacBase(String) - Static method in class biolockj.util.SeqUtil: Return regex version of IUPAC DNA substitution bases so that only ACGT values are used.
getJobParams() - Method in class biolockj.module.report.r.R_Module: If running Docker, run the Docker bash script, otherwise:
Run Config."exe.Rscript" command on the generated R Script: ScriptModuleImpl.getMainScript().
getJobParams() - Method in interface biolockj.module.ScriptModule: Many ScriptModules generate bash or R scripts for the Operating System to run as a Processor.
The Processor creates a Process using the parameters supplied by this method and executed in the Runtime environment.
Parameters typically contain the full script path and script parameters, if needed.
getJobParams() - Method in class biolockj.module.ScriptModuleImpl
getLatestColumnName(String) - Static method in class biolockj.util.MetaUtil: Returns the latest version of the given column.
getLevel() - Method in class biolockj.node.JsonNode: Getter method for level
getLevel(String) - Method in class biolockj.node.r16s.QiimeNode: Get the first taxonomy level delim.
getLevelTaxaCounts(TreeMap<String, TreeMap<String, Long>>, String) - Static method in class biolockj.util.TaxaUtil: Return TreeMap keyed on Sample ID, each sample maps to an inner map(taxa, count).
Input param sampleOtuCounts contains OTUs for which many can share the same level taxonomy assignment.
For example if sample42 contained the following 3 OTU values: phylum__Actinobacteria|class__Actinobacteria|order__Actinomycetales|family__Actinomycetaceae|genus__Actinomyces 1000 phylum__Bacteroidetes|class__Bacteroidia|order__Bacteroidales|family__Porphyromonadaceae|genus__Barnesiella 500 phylum__Bacteroidetes|class__Bacteroidia|order__Bacteroidales|family__Porphyromonadaceae|genus__Parabacteroides 77 The phylum level output would contain entries: TreeMap(sample42, TreeMap( Actinobacteria=1000, Bacteroidetes=577 ) )
getLine() - Method in interface biolockj.node.OtuNode: Get the line from classifier output file used to create this OtuNode.
getLine() - Method in class biolockj.node.OtuNodeImpl
getList(BioModule, String) - Static method in class biolockj.Config: Parse comma delimited property value to return list
getLocalDir(String) - Static method in class biolockj.util.BioLockJUtil: Return directory for path after modifying if running in a Docker container and/or interpreting bash env vars.
getLocalFile(String) - Static method in class biolockj.util.BioLockJUtil: Return file for path after modifying if running in a Docker container and/or interpreting bash env vars.
getLogBase() - Method in class biolockj.module.report.taxa.NormalizeTaxaTables: Get the Log base (10 or e)
getLowAbundantSamples() - Method in class biolockj.module.report.otu.RarefyOtuCounts: Return a list of low abundant samples, as defined by "rarefyOtuCounts.lowAbundantCutoff"
getMainNf() - Static method in class biolockj.util.NextflowUtil: Get the Nextflow main.nf file path.
getMainR() - Static method in class biolockj.module.report.r.R_Module: Get the main R script
getMainScript() - Method in interface biolockj.module.ScriptModule: Method returns MAIN module script that calls each of the worker scripts.
getMainScript() - Method in class biolockj.module.ScriptModuleImpl: Get the main script file in the bioModule script directory, with prefix: "MAIN_".
getMainScriptExecuteWorkerLine(ScriptModule, String, String) - Static method in class biolockj.util.BashScriptBuilder: Call "execute" on the worker script
getMasterConfig() - Static method in class biolockj.util.PropUtil: Return the MASTER config file.
getMaxOtusPerSample() - Method in class biolockj.module.report.otu.CompileOtuCounts: Find the maximum OTU count per sample.
getMean(Collection<?>, boolean) - Static method in class biolockj.util.SummaryUtil: Return the mean value
getMedian(Collection<?>, boolean) - Static method in class biolockj.util.SummaryUtil: Return the median value
getMergedLine(String) - Method in class biolockj.module.report.humann2.AddMetadataToPathwayTables: Return OTU table line with metadata row appended (both have PK = sample ID)
getMergedLine(String) - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables: Return OTU table line with metadata row appended (both have PK = sample ID)
getMetadata(BioModule) - Static method in class biolockj.Pipeline: If the bioModule is complete and contains a metadata file in its output directory, return the metadata file, since it must be a new version.
getMetadata() - Static method in class biolockj.util.MetaUtil: Metadata file getter.
getMetaMergedModule() - Method in class biolockj.module.report.r.R_Module: Get correct meta-merged BioModule type for the give module.
getMinOtusPerSample() - Method in class biolockj.module.report.otu.CompileOtuCounts: Find the minimum OTU count per sample.
getModule(BioModule, String, boolean) - Static method in class biolockj.util.ModuleUtil: Get a module with given className unless a classifier module is found 1st.
Use checkAhead parameter to determine if we look forward or backwards starting from the given module.
getModule(String) - Static method in class biolockj.util.ModuleUtil: Construct a BioModule based on its className.
getModuleDir() - Method in interface biolockj.module.BioModule: Each BioModule generates sub-directory under $DOCKER_PROJ
getModuleDir() - Method in class biolockj.module.BioModuleImpl: All BioModule work must be contained within the scope of its root directory.
getModuleNumber() - Static method in class biolockj.util.SummaryUtil: Read the summary file to find the last completed module number and return the next number.
getModuleProp(BioModule, String) - Static method in class biolockj.Config: Return module specific property if configured, otherwise use the given prop.
getModuleProp(String, String) - Static method in class biolockj.Config: Return module specific property if configured, otherwise use the given prop.
getModuleRunTime(BioModule) - Static method in class biolockj.util.SummaryUtil: Return duration module ran based on modified data of started file, formatted for display (as hours, minutes, seconds).
getModules() - Static method in class biolockj.Pipeline: Return a list of BioModules constructed by the BioModuleFactory
getModules(BioModule, Boolean) - Static method in class biolockj.util.ModuleUtil: Return pipeline modules after the given module if checkAhead = TRUE
Otherwise return pipeline modules before the given module.
If returning the prior modules, return the pipeline modules in reverse order, so the 1st item in the list is the module immediately preceding the given module.
getModuleScript() - Method in class biolockj.module.report.r.R_Module: Get the Module script
getMsgs() - Static method in class biolockj.Log: Get the logMesseges created prior to creating the actual Log.LOG_FILE
getNextflowLines(File) - Static method in class biolockj.util.NextflowUtil: Build the main.nf lines from the template file by replacing several parameters.
getNextModule(BioModule) - Static method in class biolockj.util.ModuleUtil: BioModules are run in the order configured.
Return the module configured to run after the given module.
getNonNegativeInteger(BioModule, String) - Static method in class biolockj.Config: Parse property as non-negative integer value
getNumLinesPerRead() - Static method in class biolockj.util.SeqUtil: Return number of lines per read (for fasta return 2, for fastq return 4)
getNumOtusForQuantile(TreeMap<String, TreeMap<String, Long>>) - Method in class biolockj.module.report.otu.RarefyOtuCounts: Get the quantile number of OTUs.
getNumReadFieldName() - Static method in class biolockj.module.implicit.RegisterNumReads: Getter for numReadFieldName
getNumReads(long) - Static method in class biolockj.util.SeqUtil: Return number of reads given number of lines in a sample.
getOtu() - Method in class biolockj.util.OtuUtil.OtuCountLine: Get OTU name
getOtuCountField() - Static method in class biolockj.module.implicit.parser.ParserModuleImpl: Getter for otuCountField
getOtuCountFile(File, String, String) - Static method in class biolockj.util.OtuUtil: Build OTU count file using a standard format in the directory given.
Format: pipeline_name + prefix + "otuCount" + sampleId + ".tsv"
getOtuCounts() - Method in class biolockj.node.ParsedSample: Get the streamlined taxonomy tree with counts, each OTU listed only 1 time with num occurrences in the sample.
Example: d__Bacteria;p__Bacteroidetes;c__Bacteroidia;o__Bacteroidales;f__Bacteroidaceae;g__Bacteroides;s__Bacteroides_vulgatus 87342
getOtuName() - Method in interface biolockj.node.OtuNode: Build the OTU name from the taxaMap.
getOtuName() - Method in class biolockj.node.OtuNodeImpl
getOtuNames(String) - Static method in class biolockj.module.report.taxa.NormalizeTaxaTables: Parse Taxa names from the given header line.
getOtuTableRowId(String) - Static method in class biolockj.module.implicit.parser.r16s.QiimeParser: This method is used to get an R-friendly Sample ID value by stripping out the quotes AND by replacing any Qiime ID found with the original Sample ID.
getOutputDir() - Method in interface biolockj.module.BioModule: Output files destined as input for the next BioModule is created in this directory.
getOutputDir() - Method in class biolockj.module.BioModuleImpl: Returns moduleDir/output which will be used as the next module's input.
getOutputDirSummary(BioModule) - Static method in class biolockj.util.SummaryUtil: Return summary of BioModule output directory, with metrics: Number of output files Mean output file size Path of new metadata file if any created
getPad(String) - Static method in class biolockj.util.SummaryUtil: Summary count label padding as label length + 18
getPairedReads(Collection<File>) - Static method in class biolockj.util.SeqUtil: Paired reads must have a unique file suffix to identify forward and reverse reads.
getParams() - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier: Metaphlan queries require standard parameters: --input_type, --nproc, -t
Verify no invalid runtime params are passed and add rankSwitch if needed.
Set the rankSwitch based on the Config."report.taxonomyLevels" if only one taxonomy level is to be reported, otherwise report all levels.
getParams() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: Subclasses call this method to check dependencies before picking OTUs to validate Config."qiime.params"
getParent() - Method in class biolockj.node.JsonNode: Getter method for parent
getParsedSample(String) - Method in interface biolockj.module.implicit.parser.ParserModule: After ParserModule.parseSamples() completes, this method can be called to get a ParsedSample by its sample ID.
getParsedSample(String) - Method in class biolockj.module.implicit.parser.ParserModuleImpl
getPath() - Static method in class biolockj.util.MetaUtil: Return the metadata file path
getPathwayCountFile(File, File, String) - Static method in class biolockj.util.PathwayUtil: Return a pathway abundance file path in the given dir with the given prefix (if provided).
getPickOtuLines(String, File, String, File) - Method in class biolockj.module.implicit.qiime.QiimeClassifier: Subclasses call this method to add OTU picking lines by calling "add_qiime_labels.py" via OTU picking script.
getPipelineInputFiles() - Static method in class biolockj.util.BioLockJUtil: Basic input files may be sequences, or any other file type acceptable in a pipeline module.
getPositiveDoubleVal(BioModule, String) - Static method in class biolockj.Config: Parse property as positive double value
getPositiveInteger(BioModule, String) - Static method in class biolockj.Config: Parse property as positive integer value
getPostRequisiteModules() - Method in interface biolockj.module.BioModule: Pipeline calls this method when building the list of pipeline BioModules to execute.
getPostRequisiteModules() - Method in class biolockj.module.BioModuleImpl: By default, no post-requisites are required.
getPostRequisiteModules() - Method in class biolockj.module.classifier.ClassifierModuleImpl: This method returns the corresponding Parser module associated with the classifier.
getPostRequisiteModules() - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier: If paired reads found, return prerequisite module: PearMergeReads.
getPostRequisiteModules() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: Subclasses of QiimeClassifier add post-requisite module: QiimeClassifier.
getPostRequisites(BioModule) - Method in class biolockj.BioModuleFactory: This method returns all module post-requisites (including post-requisites of the post-requisites).
getPreRequisiteModules() - Method in interface biolockj.module.BioModule: Pipeline calls this method when building the list of pipeline BioModules to execute.
getPreRequisiteModules() - Method in class biolockj.module.BioModuleImpl: By default, no prerequisites are required.
getPreRequisiteModules() - Method in class biolockj.module.classifier.r16s.RdpClassifier: If paired reads found, add prerequisite: PearMergeReads.
getPreRequisiteModules() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: If paired reads found, add prerequisite module: PearMergeReads.
getPreRequisiteModules() - Method in class biolockj.module.report.humann2.Humann2CountModule: Module prerequisite: Humann2Parser
getPreRequisiteModules() - Method in class biolockj.module.report.JsonReport: Module prerequisite: CompileOtuCounts
getPreRequisiteModules() - Method in class biolockj.module.report.r.R_Module: Require combined count-metadata tables as input.
getPreRequisiteModules() - Method in class biolockj.module.report.r.R_PlotEffectSize: Returns R_Module.getStatPreReqs() and if fold change plots are to be generated, add NormalizeTaxaTables
getPreRequisiteModules() - Method in class biolockj.module.report.r.R_PlotOtus: Returns R_Module.getStatPreReqs()
getPreRequisiteModules() - Method in class biolockj.module.report.r.R_PlotPvalHistograms: Returns R_Module.getStatPreReqs()
getPreRequisiteModules() - Method in class biolockj.module.report.taxa.TaxaCountModule: Require taxonomy table module as prerequisite
getPreRequisiteModules() - Method in class biolockj.module.seq.RarefySeqs: This method always requires a prerequisite module with a "number of reads" count such as: RegisterNumReads.
getPreRequisites(BioModule) - Method in class biolockj.BioModuleFactory: This method returns all module prerequisites (including prerequisites of the prerequisites).
getPreviousModule(BioModule) - Static method in class biolockj.util.ModuleUtil: BioModules are run in the order configured.
Return the module configured to run before the given module.
getPrimaryScript() - Method in class biolockj.module.report.r.R_Module: Get the primary R script
getPrimers() - Method in class biolockj.module.seq.TrimPrimers: Get the primers listed in the "trimPrimers.filePath".
getProjectName() - Static method in class biolockj.util.RuntimeParamUtil: Extract the project name from the Config file.
getProperties() - Static method in class biolockj.Config: Get current properties ordered by property
getQuotedValue(String) - Method in class biolockj.module.implicit.ImportMetadata: The member variable quotedText caches the input held within a quoted block.
getRandomQuantileOtus(List<String>, Long) - Static method in class biolockj.module.report.otu.RarefyOtuCounts: Select random OTUs based on the quantileNum from the list of OTUs in data.
getReadDirectionSuffix(File) - Static method in class biolockj.util.SeqUtil: Return read direction indicator for forward or reverse read if found in the file name.
getReadDirectionSuffix(String) - Static method in class biolockj.util.SeqUtil: Return read direction indicator for forward or reverse read if found in the file name.
getRecord(String) - Static method in class biolockj.util.MetaUtil: Get metadata row for a given Sample ID.
getRestartDir() - Static method in class biolockj.util.RuntimeParamUtil: Return restart pipeline directory
getRTemplateDir() - Static method in class biolockj.module.report.r.R_Module: Get the BioLockJ resource R directory.
getRunTime(long) - Static method in class biolockj.util.SummaryUtil: Get runtime message (formatted as hours, minutes, seconds) based on startTime passed.
getRuntimeParams() - Method in class biolockj.module.classifier.wgs.Humann2Classifier: Get formatted runtime parameters and
getRuntimeParams(List<String>, String) - Method in class biolockj.module.ScriptModuleImpl: Return all collectionProperty values separated by a space.
getSampleId(String) - Static method in class biolockj.module.implicit.parser.r16s.QiimeParser: Get the Sample ID from QiimeParser.qiimeIdToSampleIdMap.
getSampleId() - Method in interface biolockj.node.OtuNode: Gets the sample ID to which the read belongs
getSampleId() - Method in class biolockj.node.OtuNodeImpl
getSampleId() - Method in class biolockj.node.ParsedSample: Getter for sampleId.
getSampleId(List<String>) - Static method in class biolockj.util.DemuxUtil: Determine Sample Id by examining the sequence lines.
If ="id_in_header", extract the Sample Id from the sequence header via SeqUtil.getSampleId(String)
If ="barcode_in_header" and the sequence header contains a bar-code in the idMap, return the corresponding SampleID from the idMap.
If ="barcode_in_mapping" and the sequence header maps to a bar-code in the idMap, return the corresponding SampleID from the idMap.
If ="barcode_in_seq" and the sequence itself begins with a bar-code in the idMap, return the corresponding SampleID from the idMap.
getSampleId(File) - Static method in class biolockj.util.OtuUtil: Extract the sampleId from the OTU count file name.
Input files should include a file name just before the .tsv file extension.
getSampleId(String) - Static method in class biolockj.util.SeqUtil: Method extracts Sample ID from the name param.
getSampleIdFromMappingFile(String, int) - Static method in class biolockj.module.implicit.parser.r16s.QiimeParser: The mapping file used the original sampleId when generating the demultipled files, as recorded in mapping file column - "BioLockJFileName".
getSampleIds() - Method in class biolockj.module.implicit.ImportMetadata: Extract the sample IDs from the file names with SeqUtil.getSampleId(String)
getSampleIds() - Static method in class biolockj.util.MetaUtil: Get the first column from the metadata file.
getSampleOtuCounts(Collection<File>) - Static method in class biolockj.util.OtuUtil: TreeMap OTU counts for each sample file formatted and named as in ParserModule output.
getSanatizedFile(String, Boolean) - Method in class biolockj.module.seq.KneadData: Return sanitized sequence data file.
getScore() - Method in class biolockj.node.r16s.RdpNode: Return lowest RDP confidence percentage (0-100) above the configured threshold value.
getScriptDir() - Method in interface biolockj.module.ScriptModule: ScriptModules that generate scripts to complete their task, create script files in this directory.
The main script must begin with prefix and there must only be one main script.
The main script executes, or submits to the job queue, each of the other scripts in this directory.
The # subscripts generated by the ScriptModule depends upon "script.batchSize".
getScriptDir() - Method in class biolockj.module.ScriptModuleImpl: Returns moduleDir/script which contains all scripts generated by the module.
getScriptDirSummary(ScriptModule) - Static method in class biolockj.util.SummaryUtil: Return summary of the ScriptModule script directory with metrics: Print main script name Number of worker scripts run Number of worker scripts successful/failed/incomplete Average worker script run time Longest running worker script names/duration Longest running workers script names/duration
getScriptErrors() - Method in interface biolockj.module.ScriptModule: Return a list of the error messages saved the failure scripts in the module script directory.
getScriptErrors() - Method in class biolockj.module.ScriptModuleImpl: This method returns all of the lines from any failure files found in the script directory.
getScriptRunTime(Long) - Static method in class biolockj.util.SummaryUtil: Get the script runtime in hours and minutes
getSeqFiles(Collection<File>) - Method in class biolockj.module.implicit.Demultiplexer
getSeqFiles(Collection<File>) - Method in class biolockj.module.implicit.RegisterNumReads
getSeqFiles(Collection<File>) - Method in class biolockj.module.seq.AwkFastaConverter
getSeqFiles(Collection<File>) - Method in class biolockj.module.seq.Multiplexer
getSeqFiles(Collection<File>) - Method in class biolockj.module.seq.RarefySeqs
getSeqFiles(Collection<File>) - Method in class biolockj.module.seq.SeqFileValidator
getSeqFiles(Collection<File>) - Method in class biolockj.module.seq.TrimPrimers
getSeqFiles(Collection<File>) - Method in interface biolockj.module.SeqModule: Return only sequence files for sample IDs found in the metadata file.
If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.
getSeqFiles(Collection<File>) - Method in class biolockj.module.SeqModuleImpl
getSeqFiles(Collection<File>) - Static method in class biolockj.util.SeqUtil: Return only sequence files for sample IDs found in the metadata file.
If Config."metadata.required" = "Y", an error is thrown to list the files that cannot be matched to a metadata row.
getSeqHeaderChars() - Static method in class biolockj.util.SeqUtil: Get all sequence header characters for fasta and fastq files.
getSeqPrimerFile() - Static method in class biolockj.module.seq.TrimPrimers: Return the primer file.
getSeqType() - Static method in class biolockj.util.SeqUtil: Get sequence type
getSession() - Method in class biolockj.module.report.Email: Build an authenticated javax.mail.Session using Config email properties
getSet(BioModule, String) - Static method in class biolockj.Config: Parse comma-separated property value to build an unordered Set
getSource() - Method in class biolockj.module.JavaModuleImpl: Get the program source (either the jar path or main class biolockj.BioLockJ);
getSource() - Static method in class biolockj.util.BioLockJUtil: Get the source of the java runtime classes ( /bin directory or JAR file ).
getStatPreReqs() - Method in class biolockj.module.report.r.R_Module: Add R_CalculateStats to standard R_Module.getPreRequisiteModules()
getStats() - Method in class biolockj.node.JsonNode: Getter method for stats
getStatsFile(BioModule, String, Boolean, Boolean) - Static method in class biolockj.module.report.r.R_CalculateStats: Get the stats file for the given fileType and taxonomy level.
getStatus() - Static method in class biolockj.Pipeline: Return if no pipelineException has been thrown, otherwise return
getString(BioModule, String) - Static method in class biolockj.Config: Get property value as String.
getSuffix(Boolean, Boolean) - Static method in class biolockj.module.report.r.R_CalculateStats: Get the file name suffix used to specify types of statistics.
getSummary() - Method in interface biolockj.module.BioModule: Gets the BioModule execution summary, this is sent as part of the notification email, if configured.
Summary should not include data content, to avoid unintentional publication of confidential information.
However, meta-data such as number/size of files can be helpful during debug.
getSummary() - Method in class biolockj.module.BioModuleImpl: Returns summary message to be displayed by Email module so must not contain confidential info.
getSummary() - Method in class biolockj.module.classifier.ClassifierModuleImpl
getSummary() - Method in class biolockj.module.classifier.wgs.Humann2Classifier
getSummary() - Method in class biolockj.module.implicit.Demultiplexer: Produces initial count and demultiplexed output count summaries for forward/reverse reads.
getSummary() - Method in class biolockj.module.implicit.ImportMetadata: The metadata file can be updated several times during pipeline execution.
getSummary() - Method in class biolockj.module.implicit.parser.ParserModuleImpl: Produce summary message with min, max, mean, and median number of reads.
getSummary() - Method in class biolockj.module.implicit.parser.wgs.Humann2Parser
getSummary() - Method in class biolockj.module.implicit.qiime.BuildQiimeMapping: Message summarizes contents of scriptDir, and status of the QIIME mapping files (exists or not).
getSummary() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: This method extends the classifier summary by adding the Qiime OTU summary metrics.
getSummary() - Method in class biolockj.module.implicit.RegisterNumReads: Produce summary message with min, max, mean, and median number of reads.
getSummary() - Method in class biolockj.module.report.Email: Summary simply reports the status.
getSummary() - Method in class biolockj.module.report.humann2.AddMetadataToPathwayTables: Produce summary message with min, max, mean, and median hit ratios
getSummary() - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts: Produce summary message with min, max, mean, and median number of pathways.
getSummary() - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts: Produce summary message with min, max, mean, and median number of pathways.
getSummary() - Method in class biolockj.module.report.JsonReport
getSummary() - Method in class biolockj.module.report.otu.CompileOtuCounts: Add summary with unique OTU counts/level.
getSummary() - Method in class biolockj.module.report.otu.RarefyOtuCounts: Produce summary message with min, max, mean, and median number of reads.
getSummary() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts: Produce summary message with min, max, mean, and median number of reads.
getSummary() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts: Produce summary message with min, max, mean, and median number of reads.
getSummary() - Method in class biolockj.module.report.r.R_Module: Produce summary file counts for each file extension in the output directory and the number of log files in the temp directory.
getSummary() - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables: Produce summary message with min, max, mean, and median hit ratios
getSummary() - Method in class biolockj.module.report.taxa.BuildTaxaTables
getSummary() - Method in class biolockj.module.report.taxa.NormalizeTaxaTables
getSummary() - Method in class biolockj.module.ScriptModuleImpl: Returns summary message to be displayed by Email module so must not contain confidential info.
getSummary() - Method in class biolockj.module.seq.KneadData
getSummary() - Method in class biolockj.module.seq.Multiplexer: Produce a summary message with counts on total number of reads and number reads multiplexed.
getSummary() - Method in class biolockj.module.seq.PearMergeReads: Produce summary message with min, max, mean, and median number of reads.
getSummary() - Method in class biolockj.module.seq.RarefySeqs: Produce summary message with min, max, mean, and median number of reads.
getSummary() - Method in class biolockj.module.seq.SeqFileValidator: Produce a summary message with counts on total number of reads and number of valid reads containing a barcode defined in the metadata file.
getSummary() - Method in class biolockj.module.seq.TrimPrimers: Output the summary messages generated by the module.
getSummary() - Method in class biolockj.module.SeqModuleImpl: Add database info if module is a DatabaseModule
getSummary() - Static method in class biolockj.util.SummaryUtil: Pipeline execution summary.
getSummaryFile() - Static method in class biolockj.util.SummaryUtil: Getter for the summary file.
getSummaryOtuFile() - Method in class biolockj.module.report.otu.CompileOtuCounts: Get the summary output file
getSystemMetaCol(BioModule, String) - Static method in class biolockj.util.MetaUtil: Return a system generated metadata column name based on the module status.
getTaxa() - Method in class biolockj.node.JsonNode: Getter method for taxa
getTaxaByLevel(String) - Static method in class biolockj.util.TaxaUtil: Return a map of the given otu parameter split by level.
getTaxaLevels() - Static method in class biolockj.util.TaxaUtil: Method ensures taxonomy levels are returned in descending order from top to bottom.
getTaxaLevelSpan() - Static method in class biolockj.util.TaxaUtil: Return taxa levels from top to bottom level, including in-between levels not configured as part of
getTaxaMap() - Method in interface biolockj.node.OtuNode: Gets the map holding level-specific OTU names
getTaxaMap() - Method in class biolockj.node.OtuNodeImpl: This implementation ensures all levels between top and bottom taxonomy levels are complete.
getTaxaName(String, String) - Static method in class biolockj.util.TaxaUtil: Extract a taxonomy name at the given level from the given OTU.
getTaxonomyTableFile(File, String, String) - Static method in class biolockj.util.TaxaUtil: Create File object of a taxonomy table at the given level, with the given suffix, in the given directory dir.
getTaxonomyTableLevel(File) - Static method in class biolockj.util.TaxaUtil: Extract the table taxonomy level from an existing taxonomy table file.
getTempDir() - Method in interface biolockj.module.BioModule: Contains intermediate files generated by the module but not used by the next BioModule.
The files may contain supplementary information or data that may be helpful during debug or recovery.
If "pipeline.deleteTempFiles" = "Y", successful pipelines delete this directory.
getTempDir() - Method in class biolockj.module.BioModuleImpl: Returns moduleDir/temp for intermediate files.
getTimeout() - Method in class biolockj.module.report.r.R_Module: The R Script should run quickly, timeout = 10 minutes appears to work well.
getTimeout() - Method in interface biolockj.module.ScriptModule: ScriptModule that run scripts can opt to set a timeout (such as used by the R script).
getTimeout() - Method in class biolockj.module.ScriptModuleImpl: Default behavior is for scripts to run indefinitely (no timeout).
getTreeSet(BioModule, String) - Static method in class biolockj.Config: Parse comma-separated property value to build an ordered Set
getUniqueFieldValues(String, boolean) - Static method in class biolockj.util.MetaUtil: Count the number of unique values in the given field.
getUpdatedOtuCounts(TreeMap<String, TreeMap<String, Long>>, TreeMap<String, TreeSet<String>>) - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts: Remove scarce OTUs from the sampleOtuCounts and return it.
getUsedProps() - Static method in class biolockj.Config: Cache of the properties used in this pipeline.
getValidFwHeaders() - Method in class biolockj.module.implicit.Demultiplexer: Get valid forward read headers that belong to reads with a valid barcode or sample identifier.
getValidHeaders() - Method in class biolockj.module.implicit.Demultiplexer: This method obtains all valid headers for the forward reads, and returns only headers that also have a matching reverse read
getVersion() - Static method in class biolockj.util.BioLockJUtil: Method returns the current version of BioLockJ.
getVsearchParams() - Method in class biolockj.module.implicit.qiime.QiimeClassifier: Return runtime parameters for "exe.vsearchParams"
getWorkerScriptFunctions() - Method in class biolockj.module.classifier.r16s.QiimeClosedRefClassifier
getWorkerScriptFunctions() - Method in class biolockj.module.classifier.r16s.RdpClassifier: This method generates the required bash functions: "runRdp"
getWorkerScriptFunctions() - Method in class biolockj.module.classifier.wgs.Humann2Classifier
getWorkerScriptFunctions() - Method in class biolockj.module.classifier.wgs.Kraken2Classifier: This method generates the required bash function: "runKraken2"
getWorkerScriptFunctions() - Method in class biolockj.module.classifier.wgs.KrakenClassifier: This method generates the required bash functions: "translate" and "runKraken"
getWorkerScriptFunctions() - Method in class biolockj.module.classifier.wgs.Metaphlan2Classifier
getWorkerScriptFunctions() - Method in class biolockj.module.implicit.qiime.BuildQiimeMapping: This method generates the bash function used to reorder columns as per QIIME requirements: "reorderColumns"
getWorkerScriptFunctions() - Method in class biolockj.module.implicit.qiime.QiimeClassifier
getWorkerScriptFunctions() - Method in class biolockj.module.JavaModuleImpl: If in Docker mode, set "BLJ_OPTIONS" which will be reference in every worker script when running BioLockJ in direct mode.
getWorkerScriptFunctions() - Method in class biolockj.module.report.r.R_Module: This method generates the bash function that calls the R script: runScript.
getWorkerScriptFunctions() - Method in interface biolockj.module.ScriptModule: Method returns bash script lines used to build the functions called by the worker scripts.
getWorkerScriptFunctions() - Method in class biolockj.module.ScriptModuleImpl
getWorkerScriptFunctions() - Method in class biolockj.module.seq.AwkFastaConverter: This method generates the required bash functions used by the module scripts.
getWorkerScriptFunctions() - Method in class biolockj.module.seq.Gunzipper: This method generates the bash function: "openZip".
getWorkerScriptFunctions() - Method in class biolockj.module.seq.KneadData: This method generates the worker script function: "sanatizeData".
getWorkerScriptFunctions() - Method in class biolockj.module.seq.PearMergeReads: This method generates the required bash functions used by the worker scripts: "mergeReads"
getWorkerScriptLines(List<String>) - Static method in class biolockj.util.BashScriptBuilder: Pass each line and the current line number to "execute"
getWorkerScriptPath(ScriptModule, String) - Static method in class biolockj.util.BashScriptBuilder: Build the file path for the numbered worker script.
Gunzipper - Class in biolockj.module.seq: This BioModule uses gzip to decompress input sequence files.
Gunzipper() - Constructor for class biolockj.module.seq.Gunzipper
GZIP_EXT - Static variable in class biolockj.Constants: Gzip compressed file extension constant: ".gz"
GZIP_EXT - Static variable in class biolockj.module.BioModuleImpl: BioLockJ gzip file extension constant: ".gz"

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