All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class FilterGVCFPlugin
extends AbstractPlugin
                    
```

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
`FilterGVCFPlugin(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()`
`String`	`refFile()`	Reference File used to create the GVCFs.
`FilterGVCFPlugin`	`refFile(String value)`	Set Ref File.
`String`	`bedFile()`	Bed file containing the gene information.
`FilterGVCFPlugin`	`bedFile(String value)`	Set Bed File.
`String`	`gVCFInputDir()`	Directory holding the GVCF files to be filtered.
`FilterGVCFPlugin`	`gVCFInputDir(String value)`	Set Gvcf Dir.
`String`	`outputDir()`	Directory to hold the output files.
`FilterGVCFPlugin`	`outputDir(String value)`	Set Output Dir.
`String`	`configFile()`	Config folder containing the filtering parameters.
`FilterGVCFPlugin`	`configFile(String value)`	Set Config File.
`Double`	`lowerPoissonBound()`	Lower Poisson Bound used for filtering.
`FilterGVCFPlugin`	`lowerPoissonBound(Double value)`	Set Lower Poisson Bound.
`Double`	`upperPoissonBound()`	Upper Poisson Bound used for filtering.
`FilterGVCFPlugin`	`upperPoissonBound(Double value)`	Set Upper Poisson Bound.

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
  - FilterGVCFPlugin
```
FilterGVCFPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - refFile
```
 String refFile()
```
    Reference File used to create the GVCFs.
  - refFile
```
 FilterGVCFPlugin refFile(String value)
```
    Set Ref File. Reference File used to create the GVCFs.
    
    Parameters:
    
    value - Ref File
  - bedFile
```
 String bedFile()
```
    Bed file containing the gene information.
  - bedFile
```
 FilterGVCFPlugin bedFile(String value)
```
    Set Bed File. Bed file containing the gene information.
    
    Parameters:
    
    value - Bed File
  - gVCFInputDir
```
 String gVCFInputDir()
```
    Directory holding the GVCF files to be filtered.
  - gVCFInputDir
```
 FilterGVCFPlugin gVCFInputDir(String value)
```
    Set Gvcf Dir. Directory holding the GVCF files to be filtered.
    
    Parameters:
    
    value - Gvcf Dir
  - outputDir
```
 String outputDir()
```
    Directory to hold the output files.
  - outputDir
```
 FilterGVCFPlugin outputDir(String value)
```
    Set Output Dir. Directory to hold the output files.
    
    Parameters:
    
    value - Output Dir
  - configFile
```
 String configFile()
```
    Config folder containing the filtering parameters.
  - configFile
```
 FilterGVCFPlugin configFile(String value)
```
    Set Config File. Config folder containing the filtering parameters.
    
    Parameters:
    
    value - Config File
  - lowerPoissonBound
```
 Double lowerPoissonBound()
```
    Lower Poisson Bound used for filtering.
  - lowerPoissonBound
```
 FilterGVCFPlugin lowerPoissonBound(Double value)
```
    Set Lower Poisson Bound. Lower Poisson Bound used for filtering.
    
    Parameters:
    
    value - Lower Poisson Bound
  - upperPoissonBound
```
 Double upperPoissonBound()
```
    Upper Poisson Bound used for filtering.
  - upperPoissonBound
```
 FilterGVCFPlugin upperPoissonBound(Double value)
```
    Set Upper Poisson Bound. Upper Poisson Bound used for filtering.
    
    Parameters:
    
    value - Upper Poisson Bound

Class FilterGVCFPlugin

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

FilterGVCFPlugin

Method Detail

processData

getIcon

getButtonName

getToolTipText

refFile

refFile

bedFile

bedFile

gVCFInputDir

gVCFInputDir

outputDir

outputDir

configFile

configFile

lowerPoissonBound

lowerPoissonBound

upperPoissonBound

upperPoissonBound