FilterGVCFSingleFilePlugin

All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class FilterGVCFSingleFilePlugin
extends AbstractPlugin
                    
```
This plugin is called from groovy script CreateHaplotypesFromBAM.groovy The gvcf remote file information will be uploaded to the db:genome_file_data table when LoadHaplotypesFromGVCFPlugin is run. So here we only need the docker/singularity specific path for storing the data. If the user is to sftp the files, then isGvcfLocal will be false, and the gvcfRemoteServer parameter will be a real server address and a path.

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
`FilterGVCFSingleFilePlugin(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`	`inputFile()`	GVCF File to be filtered.
`FilterGVCFSingleFilePlugin`	`inputFile(String value)`	Set Input G V C F File.
`String`	`outputFile()`	Output GVCF File Path and Name.
`FilterGVCFSingleFilePlugin`	`outputFile(String value)`	Set Output G V C F File.
`String`	`configFile()`	Config folder containing the filtering parameters.
`FilterGVCFSingleFilePlugin`	`configFile(String value)`	Set Config File.

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
  - FilterGVCFSingleFilePlugin
```
FilterGVCFSingleFilePlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - inputFile
```
 String inputFile()
```
    GVCF File to be filtered.
  - inputFile
```
 FilterGVCFSingleFilePlugin inputFile(String value)
```
    Set Input G V C F File. GVCF File to be filtered.
    
    Parameters:
    
    value - Input G V C F File
  - outputFile
```
 String outputFile()
```
    Output GVCF File Path and Name.
  - outputFile
```
 FilterGVCFSingleFilePlugin outputFile(String value)
```
    Set Output G V C F File. Output GVCF File Path and Name.
    
    Parameters:
    
    value - Output G V C F File
  - configFile
```
 String configFile()
```
    Config folder containing the filtering parameters.
  - configFile
```
 FilterGVCFSingleFilePlugin configFile(String value)
```
    Set Config File. Config folder containing the filtering parameters.
    
    Parameters:
    
    value - Config File