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OPTION_BARCODE_IN_HEADER - Static variable in class biolockj.util.DemuxUtil

Config property "demultiplexer.strategy" option: "barcode_in_header"

OPTION_BARCODE_IN_MAPPING - Static variable in class biolockj.util.DemuxUtil

Config property "demultiplexer.strategy" option: "barcode_in_mapping"

OPTION_BARCODE_IN_SEQ - Static variable in class biolockj.util.DemuxUtil

Config property "demultiplexer.strategy" option: "barcode_in_seq"

OPTION_DO_NOT_DEMUX - Static variable in class biolockj.util.DemuxUtil

Config property "demultiplexer.strategy" option: "do_not_demux"

OPTION_ID_IN_HEADER - Static variable in class biolockj.util.DemuxUtil

Config property "demultiplexer.strategy" option: "id_in_header"

ORDER - Static variable in class biolockj.Constants

Config option for "report.taxonomyLevels": "order"

ORDER_DELIM - Static variable in class biolockj.node.OtuNodeImpl

Standard classifier output level delimiter for ORDER

orderedQiimeIDs - Static variable in class biolockj.module.implicit.parser.r16s.QiimeParser

Qiime IDs are listed in the same order in each taxonomy level report.

OTU_COUNT - Static variable in class biolockj.Constants

Included in the file name of each file output.

OTU_SUMMARY_FILE - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

File produced by QIIME "biom summarize-table" script: "otuSummary.txt"

OTU_TABLE - Static variable in class biolockj.module.implicit.qiime.QiimeClassifier

File produced by OTU picking scripts holding read taxonomy assignments: "otu_table.biom"

OTU_TABLE_PREFIX - Static variable in class biolockj.Constants

QIIME OTU table prefix: "otu_table"

OtuCountLine(String) - Constructor for class biolockj.util.OtuUtil.OtuCountLine

Each OTU count file line has 2 parts: OTU Name and OTU Count

OtuCountModule - Class in biolockj.module.report.otu

OtuCount modules reads OTU count assignment tables (1 file/sample) with 2 columns.
Col1: Full OTU pathway spanning top to bottom level Col2: Count (# of reads) for the sample.

OtuCountModule() - Constructor for class biolockj.module.report.otu.OtuCountModule

OtuNode - Interface in biolockj.node

Classes that implement this interface store taxonomy assignment info for one sequence, as output by a classifier.

OtuNodeImpl - Class in biolockj.node

The default implementation of OtuNode is also the superclass for all WGS and 16S OtuNode classes.

OtuNodeImpl() - Constructor for class biolockj.node.OtuNodeImpl

OtuUtil - Class in biolockj.util

This utility helps work with OTU count files as formatted by the ParserModule.

OtuUtil.OtuCountLine - Class in biolockj.util

This inner class is used to hold a signle line from an OTU count file.

out(Class<?>) - Static method in class biolockj.Log

Returns the Logger for the callingClass.

OUTPUT_DIR - Static variable in interface biolockj.module.BioModule

Name of the output sub-directory

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