net.maizegenetics.pangenome.hapcollapse

Class MergeGVCFPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.hapcollapse.MergeGVCFPlugin

All Implemented Interfaces:

Runnable, net.maizegenetics.plugindef.Plugin, net.maizegenetics.plugindef.PluginListener, net.maizegenetics.util.ProgressListener

public class MergeGVCFPlugin
extends net.maizegenetics.plugindef.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

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
MergeGVCFPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	dBConfig() Config file used to set up the db connection
MergeGVCFPlugin	dBConfig(String value) Set Db Config.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	outputDir() Directory where you want to store the output VCFs
MergeGVCFPlugin	outputDir(String value) Set Output Dir.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	referenceFile() Reference Input file
MergeGVCFPlugin	referenceFile(String value) Set Reference File.

Methods inherited from class net.maizegenetics.plugindef.AbstractPlugin

addListener, cancel, convert, dataSetReturned, getCitation, getInputs, getMenu, getPanel, getParameter, getParameter, getParentFrame, getUsage, getUsageHTML, isInteractive, performFunction, pluginDescription, pluginUserManualURL, progress, progress, receiveInput, reverseTrace, run, setConfigParameters, setParameter, setParameter, setParameter, setParameters, setParametersToDefault, setThreaded, trace, wasCancelled

Methods inherited from class java.lang.Object

equals, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Methods inherited from interface net.maizegenetics.plugindef.Plugin

getPluginInstance, getPluginInstance, isPlugin

Constructor Detail

MergeGVCFPlugin

public MergeGVCFPlugin(Frame parentFrame,
                       boolean isInteractive)

Method Detail

processData

public net.maizegenetics.plugindef.DataSet processData(net.maizegenetics.plugindef.DataSet input)

Specified by:

processData in interface net.maizegenetics.plugindef.Plugin

Overrides:

processData in class net.maizegenetics.plugindef.AbstractPlugin

getIcon

public ImageIcon getIcon()

getButtonName

public String getButtonName()

getToolTipText

public String getToolTipText()

outputDir

public String outputDir()

Directory where you want to store the output VCFs

Returns:

Output Dir

outputDir

public MergeGVCFPlugin outputDir(String value)

Set Output Dir. Directory where you want to store the output VCFs

Parameters:

value - Output Dir

Returns:

this plugin

referenceFile

public String referenceFile()

Reference Input file

Returns:

Reference File

referenceFile

public MergeGVCFPlugin referenceFile(String value)

Set Reference File. Reference Input file

Parameters:

value - Reference File

Returns:

this plugin

dBConfig

public String dBConfig()

Config file used to set up the db connection

Returns:

Db Config

dBConfig

public MergeGVCFPlugin dBConfig(String value)

Set Db Config. Config file used to set up the db connection

Parameters:

value - Db Config

Returns:

this plugin