MergeGVCFPlugin

All Implemented Interfaces:

java.lang.Runnable , net.maizegenetics.plugindef.Plugin , net.maizegenetics.plugindef.PluginListener , net.maizegenetics.util.ProgressListener
```
@Deprecated() 
public class MergeGVCFPlugin
extends AbstractPlugin
                    
```
Created by zrm22 on 11/6/17. Plugin which adapts GATK's Merging GVCF files. This will simply take all the variant context records for all of the taxon at that reference range and will merge the calls and depth information into a single VariantContext record For now it will export a VCF for each reference range interval. These can then be read into the FindHaplotypeClustersPlugin The Algorithm is as follows: Take all the HaplotypeNodes: Create a GenotypeTable which has all indels expanded out to individual positions Filter out the positions where there is an indel from the GenotypeTable If outputDir is specified, export the genotypeTable using TASSEL export otherwise return the genotypeTable in a DataSet

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
`MergeGVCFPlugin(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`	`outputDir()`	Directory where you want to store the output VCFs
`MergeGVCFPlugin`	`outputDir(String value)`	Set Output Dir.
`String`	`referenceFile()`	Reference Input file
`MergeGVCFPlugin`	`referenceFile(String value)`	Set Reference File.
`String`	`dBConfig()`	Config file used to set up the db connection
`MergeGVCFPlugin`	`dBConfig(String value)`	Set Db Config.

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
  - MergeGVCFPlugin
```
MergeGVCFPlugin(Frame parentFrame, boolean isInteractive)
```
- Method Detail
  - processData
```
 DataSet processData(DataSet input)
```
  - getIcon
```
 ImageIcon getIcon()
```
  - getButtonName
```
 String getButtonName()
```
  - getToolTipText
```
 String getToolTipText()
```
  - outputDir
```
 String outputDir()
```
    Directory where you want to store the output VCFs
  - outputDir
```
 MergeGVCFPlugin outputDir(String value)
```
    Set Output Dir. Directory where you want to store the output VCFs
    
    Parameters:
    
    value - Output Dir
  - referenceFile
```
 String referenceFile()
```
    Reference Input file
  - referenceFile
```
 MergeGVCFPlugin referenceFile(String value)
```
    Set Reference File. Reference Input file
    
    Parameters:
    
    value - Reference File
  - dBConfig
```
 String dBConfig()
```
    Config file used to set up the db connection
  - dBConfig
```
 MergeGVCFPlugin dBConfig(String value)
```
    Set Db Config. Config file used to set up the db connection
    
    Parameters:
    
    value - Db Config