All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class CreateSmallGenomesPlugin
extends AbstractPlugin
                    
```
This class provides a standalone plugin to create the small sequence test genome files. Files are stored as per relative paths defined in SmallSeqPaths.java This plugin also creates reference index files as may be neede by BWA, GATK or other methods. Currently there are no required parameters - each parameter has a default. NOTE: This plugin creates the indices needed, so if the user is not running through RUnSmallSeqTestsDocker, the path to samtools, bwa and picard must be given. If running from a CBSU machine, these are: /programs/bin/bwa/bwa /programs/bin/picard-tools/picard /programs/bin/samtools/samtools To run this plugin on a cbsu machine using default parameters except for the indexes tools, do this (replace your own

Nested Class Summary

Nested Classes
Modifier and Type	Class	Description

Field Summary

Fields
Modifier and Type	Field	Description
`public final static String`	`DEFAULT_CITATION`
`public final static String`	`POSITION_LIST_NONE`
`public final static String`	`TAXA_LIST_NONE`

Constructor Summary

Constructors
Constructor	Description
`CreateSmallGenomesPlugin()`
`CreateSmallGenomesPlugin(Frame parentFrame)`
`CreateSmallGenomesPlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`static void`	`main(Array<String> args)`
`Integer`	`geneLength()`	Number of base pairs to include for each gene region
`CreateSmallGenomesPlugin`	`geneLength(Integer value)`	Set Length Of Genes.
`Integer`	`interGeneLength()`	Number of base pairs to include for each intergenic region
`CreateSmallGenomesPlugin`	`interGeneLength(Integer value)`	Set Length Of Inter Genes.
`Integer`	`numberOfGenes()`	Number of gene regions to create
`CreateSmallGenomesPlugin`	`numberOfGenes(Integer value)`	Set Number Of Genes.
`Integer`	`readLength()`	Desired length of reads for fastq files
`CreateSmallGenomesPlugin`	`readLength(Integer value)`	Set Length Of Reads.
`Integer`	`hapDivergence()`	Percent each haplotype sequence should diverge from reference
`CreateSmallGenomesPlugin`	`hapDivergence(Integer value)`	Set Haplotype Divergence.
`Integer`	`interHapDivergence()`	Percent each haplotype sequence should diverge from reference
`CreateSmallGenomesPlugin`	`interHapDivergence(Integer value)`	Set Inter-Haplotype Divergence.
`Double`	`refInterGeneDup()`	Proportion of the refererence inter-gene sequence to duplicate
`CreateSmallGenomesPlugin`	`refInterGeneDup(Double value)`	Set Proportion of InterGene Duplicate.
`Double`	`refInterGeneDelete()`	Proportion of the reference inter-gene sequence to delete
`CreateSmallGenomesPlugin`	`refInterGeneDelete(Double value)`	Set Proportion of InterGene Deleted.
`Double`	`refGeneInsert()`	Proportion of gene that will get an insertion
`CreateSmallGenomesPlugin`	`refGeneInsert(Double value)`	Set Proportion of gene that will get an insertion
`Double`	`wgsDepth()`	Depth for WGS
`CreateSmallGenomesPlugin`	`wgsDepth(Double value)`	Set WGS Depth.
`Double`	`gbsDepth()`	Depth for GBS
`CreateSmallGenomesPlugin`	`gbsDepth(Double value)`	Set GBS Depth.
`String`	`baseDirectory()`	The base directory for the small genomes data.
`CreateSmallGenomesPlugin`	`baseDirectory(String value)`	Set Base Dir.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin
addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getListeners, getMenu, getPanel, getParameter, getParentFrame, getUsage, getUsageHTML, hasListeners, isInteractive, isPluginParameter, performFunction, pluginDescription, pluginParameters, pluginUserManualURL, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameters, setParametersToDefault, setThreaded, trace, usageParameters, wasCancelled
Methods inherited from class net.maizegenetics.plugindef.Plugin
getPluginInstance, isPlugin
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

- Constructor Detail
  - CreateSmallGenomesPlugin
```
CreateSmallGenomesPlugin()
```
  - CreateSmallGenomesPlugin
```
CreateSmallGenomesPlugin(Frame parentFrame)
```
  - CreateSmallGenomesPlugin
```
CreateSmallGenomesPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - main
```
 static void main(Array<String> args)
```
  - geneLength
```
 Integer geneLength()
```
    Number of base pairs to include for each gene region
  - geneLength
```
 CreateSmallGenomesPlugin geneLength(Integer value)
```
    Set Length Of Genes. Number of base pairs to include for each gene region
    
    Parameters:
    
    value - Length Of Genes
  - interGeneLength
```
 Integer interGeneLength()
```
    Number of base pairs to include for each intergenic region
  - interGeneLength
```
 CreateSmallGenomesPlugin interGeneLength(Integer value)
```
    Set Length Of Inter Genes. Number of base pairs to include for each intergenic region
    
    Parameters:
    
    value - Length Of Inter Genes
  - numberOfGenes
```
 Integer numberOfGenes()
```
    Number of gene regions to create
  - numberOfGenes
```
 CreateSmallGenomesPlugin numberOfGenes(Integer value)
```
    Set Number Of Genes. Number of gene regions to create
    
    Parameters:
    
    value - Number Of Genes
  - readLength
```
 Integer readLength()
```
    Desired length of reads for fastq files
  - readLength
```
 CreateSmallGenomesPlugin readLength(Integer value)
```
    Set Length Of Reads. Desired length of reads for fastq files
    
    Parameters:
    
    value - Length Of Reads
  - hapDivergence
```
 Integer hapDivergence()
```
    Percent each haplotype sequence should diverge from reference
  - hapDivergence
```
 CreateSmallGenomesPlugin hapDivergence(Integer value)
```
    Set Haplotype Divergence. Percent each haplotype sequence should diverge from reference
    
    Parameters:
    
    value - Haplotype Divergence
  - interHapDivergence
```
 Integer interHapDivergence()
```
    Percent each haplotype sequence should diverge from reference
  - interHapDivergence
```
 CreateSmallGenomesPlugin interHapDivergence(Integer value)
```
    Set Inter-Haplotype Divergence. Percent each haplotype sequence should diverge from reference
    
    Parameters:
    
    value - Inter-Haplotype Divergence
  - refInterGeneDup
```
 Double refInterGeneDup()
```
    Proportion of the refererence inter-gene sequence to duplicate
  - refInterGeneDup
```
 CreateSmallGenomesPlugin refInterGeneDup(Double value)
```
    Set Proportion of InterGene Duplicate. Proportion of the refererence inter-gene sequence to duplicate
    
    Parameters:
    
    value - Proportion of InterGene Duplicate
  - refInterGeneDelete
```
 Double refInterGeneDelete()
```
    Proportion of the reference inter-gene sequence to delete
  - refInterGeneDelete
```
 CreateSmallGenomesPlugin refInterGeneDelete(Double value)
```
    Set Proportion of InterGene Deleted. Proportion of the reference inter-gene sequence to delete
    
    Parameters:
    
    value - Proportion of InterGene Deleted
  - refGeneInsert
```
 Double refGeneInsert()
```
    Proportion of gene that will get an insertion
  - refGeneInsert
```
 CreateSmallGenomesPlugin refGeneInsert(Double value)
```
    Set Proportion of gene that will get an insertion
    
    Parameters:
    
    value - length of insertions
  - wgsDepth
```
 Double wgsDepth()
```
    Depth for WGS
  - wgsDepth
```
 CreateSmallGenomesPlugin wgsDepth(Double value)
```
    Set WGS Depth. Depth for WGS
    
    Parameters:
    
    value - WGS Depth
  - gbsDepth
```
 Double gbsDepth()
```
    Depth for GBS
  - gbsDepth
```
 CreateSmallGenomesPlugin gbsDepth(Double value)
```
    Set GBS Depth. Depth for GBS
    
    Parameters:
    
    value - GBS Depth
  - baseDirectory
```
 String baseDirectory()
```
    The base directory for the small genomes data.
  - baseDirectory
```
 CreateSmallGenomesPlugin baseDirectory(String value)
```
    Set Base Dir. The base directory for the small genomes data.
    
    Parameters:
    
    value - Base Dir

Class CreateSmallGenomesPlugin

Nested Class Summary

Field Summary

Constructor Summary

Enum Constant Summary

Method Summary

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

Methods inherited from class net.maizegenetics.plugindef.Plugin

Methods inherited from class java.lang.Object

Constructor Detail

CreateSmallGenomesPlugin

CreateSmallGenomesPlugin

CreateSmallGenomesPlugin

Method Detail

processData

getIcon

getButtonName

getToolTipText

main

geneLength

geneLength

interGeneLength

interGeneLength

numberOfGenes

numberOfGenes

readLength

readLength

hapDivergence

hapDivergence

interHapDivergence

interHapDivergence

refInterGeneDup

refInterGeneDup

refInterGeneDelete

refInterGeneDelete

refGeneInsert

refGeneInsert

wgsDepth

wgsDepth

gbsDepth

gbsDepth

baseDirectory

baseDirectory