- hasColumn(String) - Static method in class biolockj.util.MetaUtil
-
Check if columnName exists in the current metadata file.
- hasDB(BioModule) - Static method in class biolockj.util.DockerUtil
-
Function used to determine if an alternate database has been defined (other than /db).
- hasExecuted(BioModule) - Static method in class biolockj.util.ModuleUtil
-
Return TRUE if module has executed.
- hashCode() - Method in class biolockj.node.JsonNode
-
- hasScripts() - Method in class biolockj.module.ScriptModuleImpl
-
Check if module produced any scripts
- hasValidBarcodes() - Static method in class biolockj.util.DemuxUtil
-
Check for the existance of the barcode column.
- HIT_RATIO - Static variable in class biolockj.module.report.taxa.AddMetadataToTaxaTables
-
- HN2_DISABLE_GENE_FAMILIES - Static variable in class biolockj.Constants
-
Config Boolean property to disable HumanN2 Gene Family report:
"humann2.disableGeneFamilies"
- HN2_DISABLE_PATH_ABUNDANCE - Static variable in class biolockj.Constants
-
Config Boolean property to disable HumanN2 Pathway Abundance report:
"humann2.disablePathAbundance"
- HN2_DISABLE_PATH_COVERAGE - Static variable in class biolockj.Constants
-
Config Boolean property to disable HumanN2 Pathway Coverage report:
"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"
Set value =
"Y" to keep UNINTEGRATED column in count tables
- HN2_KEEP_UNMAPPED - Static variable in class biolockj.module.implicit.parser.wgs.Humann2Parser
-
Config Boolean property: "humann2.keepUnmapped"
Set value =
"Y" to keep UNMAPPED column in count tables
- HN2_NUCL_DB - Static variable in class biolockj.module.classifier.wgs.Humann2Classifier
-
Config Directory property must contain the nucleotide database: "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 Directory property must contain the protein nucleotide database: "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
-
- HOST_BLJ - Static variable in class biolockj.util.RuntimeParamUtil
-
Host BioLockJ deployment to run - used to override installed $BLJ in Docker containers with BioLockJ installed:
"-blj"
- HOST_BLJ_SUP - Static variable in class biolockj.util.RuntimeParamUtil
-
Host BioLockJ deployment to run - used to map $BLJ_SUP volume in Docker containers with BioLockJ installed:
"-bljSup"
- HOST_HOME_USER_DIR - Static variable in class biolockj.util.RuntimeParamUtil
-
Host $USER $HOME param: "u"
- 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 BioModules 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
-