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H

HALT_PIPELINE - Static variable in class biolockj.util.ValidationUtil
Config boolean property "validation.stopPipeline".
handleBioLockJException(BioLockJException) - Static method in class biolockj.launch.Launcher
 
handleEndLaunchException(EndLaunch) - Static method in class biolockj.launch.Launcher
 
handleGeneralException(Exception) - Static method in class biolockj.launch.Launcher
 
hasColumn(String) - Static method in class biolockj.util.MetaUtil
Check if columnName exists in the current metadata file.
hasExecuted(BioModule) - Static method in class biolockj.util.ModuleUtil
Return TRUE if module has executed.
hashCode() - Method in class biolockj.module.BioModuleImpl
 
hashCode() - Method in class biolockj.node.JsonNode
 
hashCode() - Method in class biolockj.node.ParsedSample
 
hasMetaColToSampleIdMap() - Static method in class biolockj.util.MetaUtil
 
hasNullOrEmptyVal(Collection<Object>) - Static method in class biolockj.util.BioLockJUtil
Check collection vals for null or empty toString() values
hasPairedReads() - Static method in class biolockj.util.SeqUtil
Boolean getter for the internal Config property "internal.pairedReads".
hasScripts() - Method in class biolockj.module.ScriptModuleImpl
Check if module produced any scripts
hasScripts(BioModule) - Static method in class biolockj.util.ModuleUtil
Check a BioModule for scripts to execute.
hasStrictValidation(boolean) - Static method in class biolockj.util.ValidationUtil
Print a message (and return boolean) to indicate that this pipeline has validation enabled.
hasValidBarcodes() - Static method in class biolockj.util.DemuxUtil
Check for the existance of the barcode column.
Hello_Friends - Class in biolockj.module.hello_world
 
Hello_Friends() - Constructor for class biolockj.module.hello_world.Hello_Friends
 
Hello_World - Class in biolockj.module.hello_world
 
Hello_World() - Constructor for class biolockj.module.hello_world.Hello_World
 
HELP - Static variable in class biolockj.Constants
Argument to print help menu: "-help"
HIER_COUNTS - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
 
HIER_SUFFIX - Static variable in class biolockj.module.classifier.r16s.RdpClassifier
 
HIT_RATIO - Static variable in class biolockj.module.report.taxa.AddMetadataToTaxaTables
Metadata column name for column that stores the calculation for: ParserModuleImpl.getOtuCountField()/ RegisterNumReads.getNumReadFieldName(): "Hit_Ratio".
HN2_DISABLE_GENE_FAMILIES - Static variable in class biolockj.Constants
Config Boolean property: "humann2.disableGeneFamilies"
HN2_DISABLE_PATH_ABUNDANCE - Static variable in class biolockj.Constants
Config Boolean property: "humann2.disablePathAbundance"
HN2_DISABLE_PATH_COVERAGE - Static variable in class biolockj.Constants
Config Boolean property: "humann2.disablePathCoverage"
HN2_GENE_FAM_SUM - Static variable in class biolockj.Constants
HumanN2 file suffix identifier for Gene Family Summary report: "geneFam"
HN2_KEEP_UNINTEGRATED - Static variable in class biolockj.module.implicit.parser.wgs.Humann2Parser
Config Boolean property: "humann2.keepUnintegrated"
HN2_KEEP_UNMAPPED - Static variable in class biolockj.module.implicit.parser.wgs.Humann2Parser
Config Boolean property: "humann2.keepUnmapped"
HN2_NUCL_DB - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier
Config "file path" property: "humann2.nuclDB"
HN2_PATH_ABUND_SUM - Static variable in class biolockj.Constants
HumanN2 file suffix identifier for Pathway Abundance Summary report: "pAbund"
HN2_PATH_COVG_SUM - Static variable in class biolockj.Constants
HumanN2 file suffix identifier for Pathway Coverage Summary report: "pCovg"
HN2_PROT_DB - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier
Config "file path" property: "humann2.protDB"
HN2_TOTAL_PATH_COUNT - Static variable in class biolockj.Constants
HumanN2 meta column to store the total pathway count/sample: "Total_Pathways"
HN2_UNIQUE_PATH_COUNT - Static variable in class biolockj.Constants
HumanN2 meta column to store the unique pathway count/sample: "Total_Pathways"
HOME_DIR - Static variable in class biolockj.util.RuntimeParamUtil
Automatically added $HOME by biolockj/dockblj script: "-homeDir"
HOST_EXE_PREFIX - Static variable in class biolockj.Constants
Prefix used in several Config String properties.
howExciting() - Method in class biolockj.module.hello_world.Hello_Friends
Accesses the "hello.excitmentLevel" and creates a string with that many !s, or just "." if the value is null.
howExciting() - Method in class biolockj.module.hello_world.Step5
Accesses the "hello.excitmentLevel" and creates a string with that many !s.
howToLinkMetaWithFile - Static variable in exception biolockj.exception.MetadataException
 
Humann2Classifier - Class in biolockj.module.classifier.wgs
This BioModule runs biobakery humann2 program to generate the HMP Unified Metabolic Analysis Network
HUMAnN is a pipeline for efficiently and accurately profiling the presence/absence and abundance of microbial pathways in a community from metagenomic or metatranscriptomic sequencing data (typically millions of short DNA/RNA reads).
Humann2Classifier() - Constructor for class biolockj.module.classifier.wgs.Humann2Classifier
 
Humann2CountModule - Class in biolockj.module.report.humann2
This abstract superclass is extended by all other modules in this package.
Shared method implementations are defined to ensure uniform adoption of dependencies and prerequisites.
Humann2CountModule() - Constructor for class biolockj.module.report.humann2.Humann2CountModule
 
Humann2Parser - Class in biolockj.module.implicit.parser.wgs
This BioModule parses Humann2Classifier output reports to build standard OTU abundance tables.
Samples IDs are found in the column headers starting with the 2nd column.
The count type depends on the HumanN2 config properties.
Humann2Parser() - Constructor for class biolockj.module.implicit.parser.wgs.Humann2Parser
 
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