FilterFastqUsingBAMPlugin

All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
public class FilterFastqUsingBAMPlugin
extends AbstractPlugin
                    
```
Created by zrm22 on 9/13/17.

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
`FilterFastqUsingBAMPlugin(Frame parentFrame, boolean isInteractive)`

Enum Constant Summary

Enum Constants
Enum Constant	Description

Method Summary

Modifier and Type	Method	Description
`DataSet`	`processData(DataSet input)`
`String`	`pluginUserManualURL()`
`ImageIcon`	`getIcon()`
`String`	`getButtonName()`
`String`	`getToolTipText()`
`String`	`reference()`	File Name of the reference fasta
`FilterFastqUsingBAMPlugin`	`reference(String value)`	Set Ref File.
`String`	`reads()`	File Name of the read fastq
`FilterFastqUsingBAMPlugin`	`reads(String value)`	Set Read File.
`String`	`bamFile()`	File Name of the bam file
`FilterFastqUsingBAMPlugin`	`bamFile(String value)`	Set Bam File.
`String`	`output()`	File Name of the filtered read output
`FilterFastqUsingBAMPlugin`	`output(String value)`	Set Output 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, 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
  - FilterFastqUsingBAMPlugin
```
FilterFastqUsingBAMPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - pluginUserManualURL
```
 String pluginUserManualURL()
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - reference
```
 String reference()
```
    File Name of the reference fasta
  - reference
```
 FilterFastqUsingBAMPlugin reference(String value)
```
    Set Ref File. File Name of the reference fasta
    
    Parameters:
    
    value - Ref File
  - reads
```
 String reads()
```
    File Name of the read fastq
  - reads
```
 FilterFastqUsingBAMPlugin reads(String value)
```
    Set Read File. File Name of the read fastq
    
    Parameters:
    
    value - Read File
  - bamFile
```
 String bamFile()
```
    File Name of the bam file
  - bamFile
```
 FilterFastqUsingBAMPlugin bamFile(String value)
```
    Set Bam File. File Name of the bam file
    
    Parameters:
    
    value - Bam File
  - output
```
 String output()
```
    File Name of the filtered read output
  - output
```
 FilterFastqUsingBAMPlugin output(String value)
```
    Set Output File. File Name of the filtered read output
    
    Parameters:
    
    value - Output File