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

R

R_ADJ_PVALS_SCOPE - Static variable in class biolockj.module.report.r.R_CalculateStats

Config String property: "r_CalculateStats.pAdjustScope" defines R p.adjust( n ) parameter.

R_CalculateStats - Class in biolockj.module.report.r

This BioModule is used to build the R script used to generate taxonomy statistics and plots.

R_CalculateStats() - Constructor for class biolockj.module.report.r.R_CalculateStats

R_COLOR_BASE - Static variable in class biolockj.module.report.r.R_Module

Config property "r.colorBase" defines the base label color

R_COLOR_HIGHLIGHT - Static variable in class biolockj.module.report.r.R_Module

Config property "r.colorHighlight" defines the highlight label color

R_COLOR_PALETTE - Static variable in class biolockj.module.report.r.R_Module

Config property "r.colorPalette" defines the color palette for PDF plots

R_COLOR_POINT - Static variable in class biolockj.module.report.r.R_Module

Config property "r.colorPoint" defines the pch point colors for PDF plots

R_DEBUG - Static variable in class biolockj.module.report.r.R_Module

Config boolean property "r.debug" sets the debug log function endabled

R_EXCLUDE_FIELDS - Static variable in class biolockj.util.RMetaUtil

Config List property: "r.excludeFields"
R reports must contain at least one valid nominal or numeric metadata field.

R_EXT - Static variable in class biolockj.Constants

File extension of BioLockJ generated R Scripts: ".R"

R_FUNCTION_LIB - Static variable in class biolockj.module.report.r.R_Module

This library script contains helper functions used in the R scripts: "BioLockJ_Lib.R"

R_INTERNAL_RUN_HN2 - Static variable in class biolockj.Constants

Config Boolean property to signal R scripts to build HumanN2 reports

R_MAIN_SCRIPT - Static variable in class biolockj.module.report.r.R_Module

This main R script that sources helper libraries and calls modules main method function: "BioLockJ_MAIN.R"

R_MDS_DISTANCE - Static variable in class biolockj.module.report.r.R_PlotMds

Config property: "r_PlotMds.distance" defines the distance index to use in the capscale command.

R_MDS_NUM_AXIS - Static variable in class biolockj.module.report.r.R_PlotMds

Config Integer property: "r_PlotMds.numAxis" defines the number of MDS axis to report

R_MDS_REPORT_FIELDS - Static variable in class biolockj.module.report.r.R_PlotMds

Config List property: "r_PlotMds.reportFields"
List metadata fields to generate MDS ordination plots.

R_MDS_REPORT_FIELDS - Static variable in class biolockj.util.RMetaUtil

Config List property: "r_PlotMds.reportFields"
Fields listed here must exist in the metadata file.

R_Module - Class in biolockj.module.report.r

This BioModule is the superclass for R script generating modules.

R_Module() - Constructor for class biolockj.module.report.r.R_Module

R_NOMINAL_FIELDS - Static variable in class biolockj.util.RMetaUtil

Config List property: "r.nominalFields"
Override default property type by explicitly listing it as nominal.

R_NUMERIC_FIELDS - Static variable in class biolockj.util.RMetaUtil

Config List property: "r.numericFields"
Override default property type by explicitly listing it as numeric.

R_PCH - Static variable in class biolockj.module.report.r.R_Module

Config property "r.pch" defines the plot point shape for PDF plots

R_PLOT_EFFECT_SIZE_DISABLE_FC - Static variable in class biolockj.Constants

Config Boolean property to disable fold change plots: "r_PlotEffectSize.disableFoldChange"

R_PlotEffectSize - Class in biolockj.module.report.r

This BioModule is used to run the R script used to generate OTU-metadata fold-change-barplots for each binary report field.

R_PlotEffectSize() - Constructor for class biolockj.module.report.r.R_PlotEffectSize

R_PlotMds - Class in biolockj.module.report.r

This BioModule is used to build the R script used to generate MDS plots for each report field and each taxonomy level configured.

R_PlotMds() - Constructor for class biolockj.module.report.r.R_PlotMds

R_PlotOtus - Class in biolockj.module.report.r

This BioModule is used to build the R script used to generate OTU-metadata box-plots and scatter-plots for each report field and taxonomy level.

R_PlotOtus() - Constructor for class biolockj.module.report.r.R_PlotOtus

R_PlotPvalHistograms - Class in biolockj.module.report.r

This BioModule is used to build the R script used to generate p-value histograms for each report field and each taxonomy level configured.

R_PlotPvalHistograms() - Constructor for class biolockj.module.report.r.R_PlotPvalHistograms

R_PVAL_ADJ_METHOD - Static variable in class biolockj.module.report.r.R_CalculateStats

Config String property: "r_CalculateStats.pAdjustMethod" defines p.adjust( method ) parameter.

R_RARE_OTU_THRESHOLD - Static variable in class biolockj.module.report.r.R_Module

Config Double property "r.rareOtuThreshold" defines number OTUs needed to includ in reports

R_REPORT_FIELDS - Static variable in class biolockj.util.RMetaUtil

Config List property: "r.reportFields"
R reports must contain at least one valid field.

R_SAVE_R_DATA - Static variable in class biolockj.module.report.r.R_Module

Config boolean property "r.saveRData" enables the .RData file to save.

R_SQUARED_VALS - Static variable in class biolockj.module.report.r.R_CalculateStats

R^2 identifier: "rSquaredVals"

R_TIMEOUT - Static variable in class biolockj.module.report.r.R_Module

Config property "r.timeout" defines the number of minutes before R script fails due to timeout.

rarefy(String, TreeMap<String, Long>, long) - Method in class biolockj.module.report.otu.RarefyOtuCounts

Rarefy the data by taking the average value of "rarefyOtuCounts.iterations"

rarefy(File) - Method in class biolockj.module.seq.RarefySeqs

Builds the rarefied file if too many seqs found, or adds files with too few samples to the list of bad samples.

RarefyOtuCounts - Class in biolockj.module.report.otu

This BioModule applies a mean iterative post-OTU classification rarefication algorithm so that each output sample will have approximately the same number of OTUs.

RarefyOtuCounts() - Constructor for class biolockj.module.report.otu.RarefyOtuCounts

RarefySeqs - Class in biolockj.module.seq

This BioModule imposes a minimum and/or maximum number of reads per sample.

RarefySeqs() - Constructor for class biolockj.module.seq.RarefySeqs

RDP_DB - Static variable in class biolockj.module.classifier.r16s.RdpClassifier

Config File property used to define an alternate RDP database file: "rdp.db"

RDP_JAR - Static variable in class biolockj.module.classifier.r16s.RdpClassifier

Config File property for RDP java executable JAR: "rdp.jar"

RDP_PARAMS - Static variable in class biolockj.module.classifier.r16s.RdpClassifier

Config List property for RDP java executable JAR runtime params: "exe.rdpParams"

RDP_THRESHOLD_SCORE - Static variable in class biolockj.Constants

Config String property: "rdp.minThresholdScore"
RdpParser will ignore OTU assignments below the threshold score (0-100)

RdpClassifier - Class in biolockj.module.classifier.r16s

This BioModule uses RDP to assign taxonomy to 16s sequences.

RdpClassifier() - Constructor for class biolockj.module.classifier.r16s.RdpClassifier

RdpNode - Class in biolockj.node.r16s

This class represents one line of RdpClassifier output.

RdpNode(String, String) - Constructor for class biolockj.node.r16s.RdpNode

Constructor called one line of RDP output.

RdpParser - Class in biolockj.module.implicit.parser.r16s

This BioModule parses RDP output files to build standard OTU abundance tables.

RdpParser() - Constructor for class biolockj.module.implicit.parser.r16s.RdpParser

readProps(File, Properties) - Static method in class biolockj.Properties

Read the properties defined in the required propFile and defaultProps (if included) to build Config.
Properties in propFile will override the defaultProps.

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

Refresh the metadata cache.

refreshOutputMetadata(BioModule) - Static method in class biolockj.Pipeline

Call MetaUtil to refresh the metadata cache if a new metadata file was output by the bioModule .

refreshRCacheIfNeeded(BioModule) - Static method in class biolockj.Pipeline

Refresh R cache if about to run the 1st R module.

RegisterNumReads - Class in biolockj.module.implicit

This BioModule parses sequence file to count the number of reads per sample.

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

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

Inspect the pipeline input files to determine if input includes paired reads.

registerRuntimeParameters(String[]) - Static method in class biolockj.util.RuntimeParamUtil

Register and verify the runtime parameters.

REMOVE_LOW_ABUNDANT_SAMPLES - Static variable in class biolockj.module.report.otu.RarefyOtuCounts

Config Boolean property "rarefyOtuCounts.rmLowSamples" if TRUE, all samples below the quantile sample are removed.

removeBadFiles() - Method in class biolockj.module.seq.SeqFileValidator

Remove sequence files in which all reads failed validation checks, leaving only an empty file.

removeColumn(String, File) - Static method in class biolockj.util.MetaUtil

Remove the metadata column from the metadata file

removeIgnoredAndEmptyFiles(Collection<File>) - Static method in class biolockj.util.BioLockJUtil

Remove ignored and empty files from the input files.

RemoveLowOtuCounts - Class in biolockj.module.report.otu

This BioModule set low OTU counts below a configured threshold to zero.
These low sample counts are assumed to be miscategorized or contaminents.

RemoveLowOtuCounts() - Constructor for class biolockj.module.report.otu.RemoveLowOtuCounts

removeLowOtuCounts(TreeMap<String, TreeMap<String, Long>>) - Method in class biolockj.module.report.otu.RemoveLowOtuCounts

Remove OTUs below the Config.

RemoveLowPathwayCounts - Class in biolockj.module.report.humann2

This BioModule set low Pathway counts below a configured threshold to zero.
These low sample counts are assumed to be miscategorized or genomic contamination.

RemoveLowPathwayCounts() - Constructor for class biolockj.module.report.humann2.RemoveLowPathwayCounts

removeLowPathwayCounts(File) - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts

Remove Pathway Counts below the Config."report.minCount"

removeOuterQuotes(String) - Static method in class biolockj.util.BioLockJUtil

Remove the outer single or double quotes of the given value.
Quotes are only removed if quotes are found as very 1st and last characters.

removeQuotes(String) - Static method in class biolockj.util.BioLockJUtil

Remove all single and double quotation marks found in value.

RemoveScarceOtuCounts - Class in biolockj.module.report.otu

This BioModule removes scarce OTUs not found in enough samples.
The OTU must be found in a configurable percentage of samples.

RemoveScarceOtuCounts() - Constructor for class biolockj.module.report.otu.RemoveScarceOtuCounts

removeScarceOtuCounts(TreeMap<String, TreeMap<String, Long>>) - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts

Output OTU count files with the updatedOtuCounts

RemoveScarcePathwayCounts - Class in biolockj.module.report.humann2

This BioModule removes scarce pathways not found in enough samples.
Each pathway must be found in a configurable percentage of samples to be retained.

RemoveScarcePathwayCounts() - Constructor for class biolockj.module.report.humann2.RemoveScarcePathwayCounts

removeScarcePathwayCounts(File, Set<String>) - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts

Remove Pathway Counts below the Config."report.minCount"

removeTempFiles() - Static method in class biolockj.BioLockJ

Delete all BioModule/"temp" folders.

REP_SET - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

Directory created by "pick_de_novo_otus.py" and "pick_open_reference_otus.py": "rep_set"

replaceEnvVar(String) - Static method in class biolockj.Config

Interpret env variable if included in the arg string, otherwise return the arg.

replaceEnvVars(Properties) - Static method in class biolockj.Config

Interpret env variables defined in the Config file and runtime env - for example
These props are used in: $BLJ/resources/config/defult/docker.properties:
BLJ_ROOT=/mnt/efs EFS_DB=${BLJ_ROOT}/db humann2.protDB=${EFS_DB}/uniref Therefore, getString( "humann2.protDB" ) returns "/mnt/efs/db/uniref"
If not found, check runtiem env (i.e., $HOME/bash_profile)

report() - Method in class biolockj.node.JsonNode

Print node info.

REPORT_LOG_BASE - Static variable in class biolockj.Constants

Config String property: "report.logBase"
Required to be set to "e" or "10" to build log normalized reports.

REPORT_MIN_COUNT - Static variable in class biolockj.Constants

Config Positive Integer property "report.minCount" defines the minimum table count allowed, if a count less that this value is found, it is set to 0.

REPORT_NUM_HITS - Static variable in class biolockj.Constants

Config Boolean property: "report.numHits"
If set to "Y", NUM_OTUS will be added to metadata file by ParserModuleImpl and included in R reports

REPORT_NUM_READS - Static variable in class biolockj.Constants

Config Boolean property: "report.numReads"
If set to "Y" and NUM_READS exists in metadata file, NUM_READS will be included in the R reports

REPORT_SAMPLE_CUTOFF - Static variable in class biolockj.Constants

Config Positive Double property "report.scarceSampleCutoff" defines minimum percentage of data columns must be non-zero to keep the sample.

REPORT_SCARCE_CUTOFF - Static variable in class biolockj.Constants

Config Positive Double property "report.scarceCountCutoff" defines minimum percentage of samples that must contain a count value for it to be kept.

REPORT_TAXONOMY_LEVELS - Static variable in class biolockj.Constants

Config List property: "report.taxonomyLevels"
This property drives a lot of BioLockJ functionality and determines which taxonomy-levels are reported.

reportAllFields(BioModule) - Static method in class biolockj.util.RMetaUtil

The override property: Config."r.reportFields" can be used to list the metadata reportable fields for use in the R modules.

reportFailure(Exception) - Static method in class biolockj.util.SummaryUtil

Report exception details in the summary

reportMemoryUsage(String) - Static method in class biolockj.util.MemoryUtil

Print stats on memory usage: Max, Total, ∆Total, %Free, Free, ∆Free.

reportSuccess(BioModule) - Static method in class biolockj.util.SummaryUtil

After each module completes, this method is called to track the execution summary.
If module is null, the pipeline is complete/successful.

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

Config Boolean property "seqFileValidator.requireEqualNumPairs" determines if module requires equal number of forward and reverse reads (simple check).

requireBoolean(BioModule, String) - Static method in class biolockj.Config

Required to return a valid boolean or

requireDoubleVal(BioModule, String) - Static method in class biolockj.Config

Requires valid double value

requireExistingDir(BioModule, String) - Static method in class biolockj.Config

Requires valid existing directory.

requireExistingDirs(BioModule, String) - Static method in class biolockj.Config

Requires valid list of file directories

requireExistingFile(BioModule, String) - Static method in class biolockj.Config

Require valid existing file

requireInteger(BioModule, String) - Static method in class biolockj.Config

Requires valid integer value

requireList(BioModule, String) - Static method in class biolockj.Config

Require valid list property

requirePositiveDouble(BioModule, String) - Static method in class biolockj.Config

Require valid positive double value

requirePositiveInteger(BioModule, String) - Static method in class biolockj.Config

Require valid positive integer value

requireSet(BioModule, String) - Static method in class biolockj.Config

Require valid Set value

requireString(BioModule, String) - Static method in class biolockj.Config

Require valid String value

requireSubDir(BioModule, String) - Static method in class biolockj.util.ModuleUtil

Get BioModule subdirectory File object with given name.

resetModuleSummary(BioModule) - Static method in class biolockj.util.SummaryUtil

Modules can be forced to reset to incomplete status.

RESTART_FLAG - Static variable in class biolockj.util.RuntimeParamUtil

Restart pipeline runtime parameter switch: "r"

RETURN - Static variable in class biolockj.Constants

Return character constant *backslash-n*

RETURN - Static variable in class biolockj.module.BioModuleImpl

Return character constant *backslash-n*

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

Return the DNA reverse compliment for the input dna parameter.

RMetaUtil - Class in biolockj.util

This utility is used to validate the metadata to help ensure the format is valid R script input.

run() - Method in class biolockj.Processor.SubProcess

runDirectModule(Integer) - Static method in class biolockj.Pipeline

If moduleName is null, run all modules, otherwise only run the specified module.

runJob(String[], String) - Method in class biolockj.Processor

Execute the command args and log output with label.

runModule() - Method in class biolockj.module.implicit.Demultiplexer

Module execution summary:
Execute Demultiplexer.breakUpFiles() to split the multiplex file into smaller size for processing Execute Demultiplexer.getValidHeaders() to obtain list of valid headers matched to sample ID with the metadata file and also verifies matching forward and reverse read headers if demuliplexing paired reads.

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

Parsers execute a task with 3 core functions: ParserModuleImpl.parseSamples() - generates ParsedSamples ParserModuleImpl.buildOtuCountFiles() - builds OTU tree tables from the ParsedSamples

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

To parse the taxonomy level reports output by QiimeClassifier: Call QiimeParser.getInputFiles() Call QiimeParser.initializeMaps() Call QiimeParser.setOrderedQiimeIDs(File) Create ParsedSample for the OtuNodeImpl.getSampleId() if not yet created.

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

runModule() - Method in class biolockj.module.implicit.RegisterNumReads

Register number of reads for each sample by parsing each file and counting number of lines.

runModule() - Method in interface biolockj.module.JavaModule

This method executes the modules primary Java routine.

runModule() - Method in class biolockj.module.JavaModuleImpl

runModule() - Method in class biolockj.module.report.humann2.AddMetadataToPathwayTables

This method matches records from the Pathway Abundance table and the metadata file by matching the sample ID value in the very 1st column (regardless of column title).

Set

runModule() - Method in class biolockj.module.report.humann2.RemoveLowPathwayCounts

runModule() - Method in class biolockj.module.report.humann2.RemoveScarcePathwayCounts

runModule() - Method in class biolockj.module.report.JsonReport

Obtain parsed sample data, build root node, and create the jsonMap by passing both to buildMap().

runModule() - Method in class biolockj.module.report.otu.CompileOtuCounts

runModule() - Method in class biolockj.module.report.otu.RarefyOtuCounts

Apply the quantile Config to the number of OTUs per sample to calculate the maximum OTU count per sample.

runModule() - Method in class biolockj.module.report.otu.RemoveLowOtuCounts

runModule() - Method in class biolockj.module.report.otu.RemoveScarceOtuCounts

runModule() - Method in class biolockj.module.report.taxa.AddMetadataToTaxaTables

This method matches records from the OTU table and the metadata file by matching the sample ID value in the very 1st column.

runModule() - Method in class biolockj.module.report.taxa.BuildTaxaTables

runModule() - Method in class biolockj.module.report.taxa.NormalizeTaxaTables

runModule() - Method in class biolockj.module.seq.Multiplexer

Execute Multiplexer.multiplex(File) on each input file

runModule() - Method in class biolockj.module.seq.RarefySeqs

For each file with number reads outside of Config.RarefySeqs.INPUT_RAREFYING_MIN and Config.RarefySeqs.INPUT_RAREFYING_MAX values, generate a new sequence file from a shuffled list of its sequences.

runModule() - Method in class biolockj.module.seq.SeqFileValidator

Cache sampleIds to compare to validated sampleIds post-processing.

runModule() - Method in class biolockj.module.seq.TrimPrimers

Trims primers from fasta or fastq files.

runPipeline() - Static method in class biolockj.BioLockJ

Execution summary:
Call Pipeline.initializePipeline() to initialize Pipeline modules For direct module execution call Pipeline.runDirectModule(Integer) Otherwise execute Pipeline.startPipeline() and save MASTER Config If Config."pipeline.deleteTempFiles" = "Y", Call BioLockJ.removeTempFiles() to delete temp files Call BioLockJ.markProjectStatus(String) to set the overall pipeline status as successful

runSubprocess(String[], String) - Static method in class biolockj.Processor

Instantiates a new Processor.
String[] array used to control spacing between command/params.
As if executing on terminal args[0] args[1]...

RuntimeParamUtil - Class in biolockj.util

This utility processes the application runtime parameters passed to BioLockJ.

RuntimeParamUtil() - Constructor for class biolockj.util.RuntimeParamUtil

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