net.maizegenetics.analysis.imputation

Class ReImputeUpdatedTaxaByFILLINPlugin

AbstractPlugin

net.maizegenetics.analysis.imputation.ReImputeUpdatedTaxaByFILLINPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class ReImputeUpdatedTaxaByFILLINPlugin
extends AbstractPlugin

Compares an unfinished HDF5 file containing raw genotypes to a corresponding unfinished HDF5 file containing FILLIN-imputed genotypes to find new taxa (or taxa with additional depth) in the raw geno file, then imputes (or reimputes) these with FILLIN and adds them to (or replaces them in) the imputed geno file. This is part of the Automated Production Pipeline.

Constructor Detail

ReImputeUpdatedTaxaByFILLINPlugin

public ReImputeUpdatedTaxaByFILLINPlugin()

ReImputeUpdatedTaxaByFILLINPlugin

public ReImputeUpdatedTaxaByFILLINPlugin(java.awt.Frame parentFrame,
                                         boolean isInteractive)

Method Detail

pluginDescription

public java.lang.String pluginDescription()

postProcessParameters

protected void postProcessParameters()

processData

public DataSet processData(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

runPlugin

public DataSet runPlugin(DataSet input)

Convenience method to run plugin with one return object.

rawHDF5GenotypeFile

public java.lang.String rawHDF5GenotypeFile()

Input, unfinished HDF5 (*.h5) file containing raw (unimputed) genotypes

Returns:

org.jetbrains.dokka.NodeRenderContent@16b76a7c: Raw HDF5 Genotype File

rawHDF5GenotypeFile

public ReImputeUpdatedTaxaByFILLINPlugin rawHDF5GenotypeFile(java.lang.String value)

Set Raw HDF5 Genotype File. Input, unfinished HDF5 (*.h5) file containing raw (unimputed) genotypes

Parameters:

value - Raw HDF5 Genotype File

Returns:

org.jetbrains.dokka.NodeRenderContent@7f41d679: this plugin

imputedHDF5GenotypeFile

public java.lang.String imputedHDF5GenotypeFile()

Target, unfinished HDF5 (*.h5) file containing imputed genotypes to be updated

Returns:

org.jetbrains.dokka.NodeRenderContent@b66b60f: Imputed HDF5 Genotype File

imputedHDF5GenotypeFile

public ReImputeUpdatedTaxaByFILLINPlugin imputedHDF5GenotypeFile(java.lang.String value)

Set Imputed HDF5 Genotype File. Target, unfinished HDF5 (*.h5) file containing imputed genotypes to be updated

Parameters:

value - Imputed HDF5 Genotype File

Returns:

org.jetbrains.dokka.NodeRenderContent@34eec21a: this plugin

donorDir

public java.lang.String donorDir()

Directory containing donor haplotype files from output of the FILLINFindHaplotypesPlugin. All files with '.gc' in the filename will be read in, only those with matching sites are used

Returns:

org.jetbrains.dokka.NodeRenderContent@1927ba71: Donor Dir

donorDir

public ReImputeUpdatedTaxaByFILLINPlugin donorDir(java.lang.String value)

Set Donor Dir. Directory containing donor haplotype files from output of the FILLINFindHaplotypesPlugin. All files with '.gc' in the filename will be read in, only those with matching sites are used

Parameters:

value - Donor Dir

Returns:

org.jetbrains.dokka.NodeRenderContent@68a44532: this plugin

positionSourceHDF5GenoFile

public java.lang.String positionSourceHDF5GenoFile()

Finished (built) HDF5 (*.h5) file to be used as a PositionList source (containing a small number of [ignored] taxa)

Returns:

org.jetbrains.dokka.NodeRenderContent@56cc40e7: Position Source HDF5 Geno File

positionSourceHDF5GenoFile

public ReImputeUpdatedTaxaByFILLINPlugin positionSourceHDF5GenoFile(java.lang.String value)

Set Position Source HDF5 Geno File. Finished (built) HDF5 (*.h5) file to be used as a PositionList source (containing a small number of [ignored] taxa)

Parameters:

value - Position Source HDF5 Geno File

Returns:

org.jetbrains.dokka.NodeRenderContent@14f0a636: this plugin

preferredHaplotypeSize

public java.lang.Integer preferredHaplotypeSize()

Preferred haplotype block size in sites (use same as in FILLINFindHaplotypesPlugin)

Returns:

org.jetbrains.dokka.NodeRenderContent@30a072eb: Preferred haplotype size

preferredHaplotypeSize

public ReImputeUpdatedTaxaByFILLINPlugin preferredHaplotypeSize(java.lang.Integer value)

Set Preferred haplotype size. Preferred haplotype block size in sites (use same as in FILLINFindHaplotypesPlugin)

Parameters:

value - Preferred haplotype size

Returns:

org.jetbrains.dokka.NodeRenderContent@7ae72c18: this plugin

keepTempGenotypes

public java.lang.Boolean keepTempGenotypes()

Keep the temporary hdf5 genotype files generated by this plugin (raw and imputed) rather than deleting them

Returns:

org.jetbrains.dokka.NodeRenderContent@4e1880db: Keep Temp Genotypes

keepTempGenotypes

public ReImputeUpdatedTaxaByFILLINPlugin keepTempGenotypes(java.lang.Boolean value)

Set Keep Temp Genotypes. Keep the temporary hdf5 genotype files generated by this plugin (raw and imputed) rather than deleting them

Parameters:

value - Keep Temp Genotypes

Returns:

org.jetbrains.dokka.NodeRenderContent@5fc84e38: this plugin