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unzip(File, String) - Static method in class biolockj.module.seq.AwkFastaConverter

Build script line to decompress gzipped sequence file.

UpdateJavaDocs - Class in biolockj.util

This class has a main() method as it is designed to be called as a stand-alone class.
This utility updates the JavaDocs to add additional header options.
These headers are added to almost every class when the JavaDoc command is run so an automated solution was needed.

UpdateJavaDocs() - Constructor for class biolockj.util.UpdateJavaDocs

updateNodeStats(LinkedHashMap<String, TreeSet<JsonNode>>, File, String, String) - Method in class biolockj.module.report.JsonReport

Add stats from R_CalculateStats into all of the JsonNodes.

updateNumAttempts() - Static method in class biolockj.util.SummaryUtil

Update the number of attempts in the summary file (called from restart)

updateRConfig(BioModule) - Static method in class biolockj.util.RMetaUtil

Get updated R config props

updateStats(String, Double) - Method in class biolockj.node.JsonNode

Update stats, add val to key name.

USE_EVERY_ROW - Static variable in class biolockj.util.MetaUtil

Config Boolean property: "metadata.useEveryRow"
If Y, require a sequence file for every SampleID (every row) in "metadata.filePath".
If N, metadata can include extraneous SampleIDs.

useHumann2RawCount(BioModule) - Static method in class biolockj.util.PathwayUtil

Determine if humann2 provided most recent raw count data, used to determine getPreReq modules.

USER_PROFILE - Static variable in class biolockj.util.LogUtil

Config File property: "pipeline.userProfile"
Bash users typically use ~/.bash_profile.

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