See: Description
| Class | Description |
|---|---|
| BashScriptBuilder |
This utility class generates the bash script files using the lines provided and
Config script
properties. |
| BioLockJUtil |
Simple utility containing String manipulation and formatting functions.
|
| DemuxUtil |
This utility contains standard methods used to handle multiplexed data.
|
| DockerUtil |
DockerUtil for Docker integration.
|
| DownloadUtil |
This utility is used to validate the metadata to help ensure the format is valid R script input.
|
| LogUtil |
This util adds auxiliary log info to BioLockJ log file
|
| MemoryUtil |
This Java memory report utility can be used to help identify memory leaks in the application.
|
| MetaUtil |
This utility is used to read, modify, or create a metadata file for the sequence data.
|
| ModuleUtil |
This utility holds general methods useful for BioModule interaction and management.
|
| NextflowUtil |
This utility builds the Nextflow main.nf used in AWS pipelines.
|
| OtuUtil |
This utility helps work with OTU count files as formatted by the
ParserModule. |
| OtuUtil.OtuCountLine |
This inner class is used to hold a signle line from an OTU count file.
|
| PathwayUtil |
This utility helps work HumanN2 pathway abundance data.
|
| PropUtil |
Simple utility containing String manipulation and formatting functions.
|
| RMetaUtil |
This utility is used to validate the metadata to help ensure the format is valid R script input.
|
| RuntimeParamUtil |
This utility processes the application runtime parameters passed to BioLockJ.
|
| SeqUtil |
This utility helps interact with FastA and FastQ sequence files.
|
| SummaryUtil |
This module builds an execution summary for the pipeline which is printed to the log file and is be sent to the user
if the Email module is configured.
|
| TaxaUtil |
This utility helps work individual Taxa names, not full OTU path files which need
OtuUtil.Taxa files containing sample taxa counts for a given taxonomy level as output by BuildTaxaTables. |
| UpdateJavaDocs |
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. |