net.maizegenetics.pangenome.db_loading

Class LoadHapSequencesFromGVCFPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.db_loading.LoadHapSequencesFromGVCFPlugin

All Implemented Interfaces:

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

public class LoadHapSequencesFromGVCFPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Plugin which will upload a GVCF file to the DB. It can be filtered or unfiltered, but will upload as haplotypes to the database. This plugin should work with GATK/Sentieon GVCFS as well as assembly GVCFs. It currently will not work with consensus. Created by Zack Miller zrm22@cornell.edu June 25th 2018

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
LoadHapSequencesFromGVCFPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	bedFile() File holding the Reference Range Information
LoadHapSequencesFromGVCFPlugin	bedFile(String value) Set Bed File.
String	dbConfigFile() File holding the DB config information
LoadHapSequencesFromGVCFPlugin	dbConfigFile(String value) Set Db Config File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	inputFile() GVCF File to be filtered.
LoadHapSequencesFromGVCFPlugin	inputFile(String value) Set Input G V C F File.
String	loadDataFile() File holding the DB config information
LoadHapSequencesFromGVCFPlugin	loadDataFile(String value) Set Load Data File.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	reference() Input Reference Fasta
LoadHapSequencesFromGVCFPlugin	reference(String value) Set Ref.

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

LoadHapSequencesFromGVCFPlugin

public LoadHapSequencesFromGVCFPlugin(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()

inputFile

public String inputFile()

GVCF File to be filtered.

Returns:

Input G V C F File

inputFile

public LoadHapSequencesFromGVCFPlugin inputFile(String value)

Set Input G V C F File. GVCF File to be filtered.

Parameters:

value - Input G V C F File

Returns:

this plugin

reference

public String reference()

Input Reference Fasta

Returns:

Ref

reference

public LoadHapSequencesFromGVCFPlugin reference(String value)

Set Ref. Input Reference Fasta

Parameters:

value - Ref

Returns:

this plugin

dbConfigFile

public String dbConfigFile()

File holding the DB config information

Returns:

Db Config File

dbConfigFile

public LoadHapSequencesFromGVCFPlugin dbConfigFile(String value)

Set Db Config File. File holding the DB config information

Parameters:

value - Db Config File

Returns:

this plugin

loadDataFile

public String loadDataFile()

File holding the DB config information

Returns:

Load Data File

loadDataFile

public LoadHapSequencesFromGVCFPlugin loadDataFile(String value)

Set Load Data File. File holding the DB config information

Parameters:

value - Load Data File

Returns:

this plugin

bedFile

public String bedFile()

File holding the Reference Range Information

Returns:

Bed File

bedFile

public LoadHapSequencesFromGVCFPlugin bedFile(String value)

Set Bed File. File holding the Reference Range Information

Parameters:

value - Bed File

Returns:

this plugin