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

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