net.maizegenetics.pangenome.gvcfFiltering

Class FilterGVCFPlugin

java.lang.Object

net.maizegenetics.plugindef.AbstractPlugin

net.maizegenetics.pangenome.gvcfFiltering.FilterGVCFPlugin

All Implemented Interfaces:

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

public class FilterGVCFPlugin
extends net.maizegenetics.plugindef.AbstractPlugin

Created by zrm22 on 10/30/17. Plugin to run the FilterGVCF process. Will both filter the gvcfs and will export a fasta file which is used for DB uploading It is highly suggested to use the configFile as it provides more flexibility with the filtering process. The parameters for the configuration file are as follows: exclusionString = String used for bcftools filtering. If this is specified, no additional terms are added to exclude DP_poisson_min = minimum poisson bound used for filtering(absolute minimum is 0.0) DP_poisson_max = maximum poisson bound used for filtering(absolute maximum is 1.0) DP_min = minimum DP bound DP_max = maximum DP bound GQ_min = minimum GQ bound GQ_max = maximum GQ bound QUAL_min = base quality minimum bound QUAL_max = base quality maximum bound filterHets = true/false or t/f, if true will filter sites where 2 or more alleles have above 0 AD If any are left out, the plugin will just ignore that condition Using the exclusionString will allow for greater filtering control as you can specify any VCF annotation.

Field Summary

Fields inherited from class net.maizegenetics.plugindef.AbstractPlugin

DEFAULT_CITATION, POSITION_LIST_NONE, TAXA_LIST_NONE

Constructor Summary

Constructors

Constructor and Description
FilterGVCFPlugin(Frame parentFrame, boolean isInteractive)

Method Summary

Modifier and Type	Method and Description
String	bedFile() Bed file containing the gene information.
FilterGVCFPlugin	bedFile(String value) Set Bed File.
String	configFile() Config folder containing the filtering parameters.
FilterGVCFPlugin	configFile(String value) Set Config File.
String	getButtonName()
ImageIcon	getIcon()
String	getToolTipText()
String	gVCFInputDir() Directory holding the GVCF files to be filtered.
FilterGVCFPlugin	gVCFInputDir(String value) Set Gvcf Dir.
Double	lowerPoissonBound() Lower Poisson Bound used for filtering.
FilterGVCFPlugin	lowerPoissonBound(Double value) Set Lower Poisson Bound.
String	outputDir() Directory to hold the output files.
FilterGVCFPlugin	outputDir(String value) Set Output Dir.
net.maizegenetics.plugindef.DataSet	processData(net.maizegenetics.plugindef.DataSet input)
String	refFile() Reference File used to create the GVCFs.
FilterGVCFPlugin	refFile(String value) Set Ref File.
Double	upperPoissonBound() Upper Poisson Bound used for filtering.
FilterGVCFPlugin	upperPoissonBound(Double value) Set Upper Poisson Bound.

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

FilterGVCFPlugin

public FilterGVCFPlugin(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()

refFile

public String refFile()

Reference File used to create the GVCFs.

Returns:

Ref File

refFile

public FilterGVCFPlugin refFile(String value)

Set Ref File. Reference File used to create the GVCFs.

Parameters:

value - Ref File

Returns:

this plugin

bedFile

public String bedFile()

Bed file containing the gene information.

Returns:

Bed File

bedFile

public FilterGVCFPlugin bedFile(String value)

Set Bed File. Bed file containing the gene information.

Parameters:

value - Bed File

Returns:

this plugin

gVCFInputDir

public String gVCFInputDir()

Directory holding the GVCF files to be filtered.

Returns:

Gvcf Dir

gVCFInputDir

public FilterGVCFPlugin gVCFInputDir(String value)

Set Gvcf Dir. Directory holding the GVCF files to be filtered.

Parameters:

value - Gvcf Dir

Returns:

this plugin

outputDir

public String outputDir()

Directory to hold the output files.

Returns:

Output Dir

outputDir

public FilterGVCFPlugin outputDir(String value)

Set Output Dir. Directory to hold the output files.

Parameters:

value - Output Dir

Returns:

this plugin

configFile

public String configFile()

Config folder containing the filtering parameters.

Returns:

Config File

configFile

public FilterGVCFPlugin configFile(String value)

Set Config File. Config folder containing the filtering parameters.

Parameters:

value - Config File

Returns:

this plugin

lowerPoissonBound

public Double lowerPoissonBound()

Lower Poisson Bound used for filtering.

Returns:

Lower Poisson Bound

lowerPoissonBound

public FilterGVCFPlugin lowerPoissonBound(Double value)

Set Lower Poisson Bound. Lower Poisson Bound used for filtering.

Parameters:

value - Lower Poisson Bound

Returns:

this plugin

upperPoissonBound

public Double upperPoissonBound()

Upper Poisson Bound used for filtering.

Returns:

Upper Poisson Bound

upperPoissonBound

public FilterGVCFPlugin upperPoissonBound(Double value)

Set Upper Poisson Bound. Upper Poisson Bound used for filtering.

Parameters:

value - Upper Poisson Bound

Returns:

this plugin