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V

VALIDATED_MAPPING - Static variable in class biolockj.module.implicit.qiime.BuildQiimeMapping

Suffix appended to the validate QIIME mapping file output to temp/mapping dir by bash script

validateFile(File, Integer) - Method in class biolockj.module.seq.SeqFileValidator

Validate sequence files: Validate valid 1st sequence header character is expected character Validate fastq files have same number of bases and quality scores per read Remove reads below minimum threshold: "seqFileValidator.seqMinLen" Trim reads if above the maximum threshold: "seqFileValidator.seqMaxLen" Invalid reads are saved to a file in the module temp directory for analysis/review.

validateLogLevel() - Static method in class biolockj.Log

Validate log level is configured to one of the valid Log4J options: DEBUG, INFO, WARN, ERROR

validateModule(BioModule) - Static method in class biolockj.util.ValidationUtil

validateModuleOrder() - Method in class biolockj.module.classifier.ClassifierModuleImpl

Validate that no biolockj.module.seq modules run after this classifier unless a new classifier branch is started.

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

Validate that no biolockj.module.seq modules run after this parser unless a new classifier branch is started.

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

This method ensures that the multiplexed data is not passed to other modules.
This must be the last module, or last module before the Email.

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

VALIDATION_ENABLED - Static variable in class biolockj.Constants

String used by sheepdog_testing_suite to assert that validation is enabled: "This pipeline has validation enabled.".

VALIDATION_FOLDER - Static variable in class biolockj.util.ValidationUtil

ValidationException - Exception in biolockj.exception

ValidationException is thrown at module runtime if the Validation module finds a discrepancy between the expectations given for one or more files and the files found in the previous module.

ValidationException(BioModule) - Constructor for exception biolockj.exception.ValidationException

Generate BioModule specific error message.

ValidationException(String) - Constructor for exception biolockj.exception.ValidationException

Default error message (not BioModule specific).

ValidationExecutionException - Exception in biolockj.exception

ValidationException is thrown at module runtime if the ValidationUtil throws a non-BioLockJ error while validating module output.

ValidationExecutionException(BioModule) - Constructor for exception biolockj.exception.ValidationExecutionException

Generate BioModule specific error message.

ValidationExecutionException(String) - Constructor for exception biolockj.exception.ValidationExecutionException

Default error message (not BioModule specific).

ValidationUtil - Class in biolockj.util

This utility measures attributes of the files in the output directory of each module as it completes.

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

ValidationUtilityException - Exception in biolockj.exception

ValidationUtilityException(Exception, String) - Constructor for exception biolockj.exception.ValidationUtilityException

verifyAllRowsMapToSeqFile(List<File>) - Method in class biolockj.module.implicit.ImportMetadata

Verify every row (every Sample ID) maps to a sequence file

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

Verify the HumanN2 Config contains at least one of the following reports are enabled:
"humann2.disableGeneFamilies" "humann2.disablePathCoverage" "humann2.disableGeneFamilies"

verifyHeader(String, List<String>, int) - Static method in class biolockj.module.implicit.ImportMetadata

Verify column headers are not null and unique

verifyMetadataFieldsExist(BioModule, String, Collection<String>) - Static method in class biolockj.util.RMetaUtil

This method verifies the fields given exist in the metadata file.

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

Verify equal number of forward and reverse read files.
if "seqFileValidator.requireEqualNumPairs"="Y", verify forward and reverse read files have an equal number of reads.

VERSION - Static variable in class biolockj.Constants

BioLockJ main() runtime arg used to print version info: "-version"

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

Changes to a module class should be accompanied by a increment in version.

version() - Method in class biolockj.module.classifier.r16s.RdpClassifier

version() - Method in class biolockj.module.diversity.ShannonDiversity

version() - Method in class biolockj.module.diy.ForEachFile

version() - Method in class biolockj.module.diy.ForEachLevel

Deprecated.

version() - Method in class biolockj.module.diy.ForEachLoop

version() - Method in class biolockj.module.diy.ForEachSample

version() - Method in class biolockj.module.diy.GenMod

version() - Method in class biolockj.module.getData.sra.SraDownload

version() - Method in class biolockj.module.implicit.parser.r16s.RdpHierParser

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

version() - Method in class biolockj.module.report.Email

version() - Method in class biolockj.module.report.r.R_PlotMds

version() - Method in class biolockj.module.report.r.R_PlotPvalHistograms

version() - Method in class biolockj.module.report.taxa.NormalizeByReadsPerMillion

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

version() - Method in class biolockj.module.Stop

version() - Method in class biolockj.util.paths.CommonDockerMapper

version() - Method in interface biolockj.util.paths.DockerMountMapper

Changes to a mapper class should be accompanied by a increment in version.

version() - Method in class biolockj.util.paths.SimpleDockerMapper

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