- 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
-
- 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
-
- 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
-