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

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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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