net.maizegenetics.analysis.imputation

Class FindMergeHaplotypesPlugin

AbstractPlugin

net.maizegenetics.analysis.imputation.FindMergeHaplotypesPlugin

All Implemented Interfaces:

Plugin, PluginListener, ProgressListener

public class FindMergeHaplotypesPlugin
extends AbstractPlugin

Creates haplotypes by finding large IBS regions within GBS data. Starts with the highest coverage taxa and looks within windows of near perfect matches. Combines all matches together into one haplotype. The haplotype is named for the highest coverage sample. TODO: 1. plus add short inbred segments not present full ones 2. Cluster and choose haplotypes by cluster and number of new minor alleles (or information) 3. Set max het frequency as a setting

Constructor Detail

FindMergeHaplotypesPlugin

public FindMergeHaplotypesPlugin()

FindMergeHaplotypesPlugin

public FindMergeHaplotypesPlugin(java.awt.Frame parentFrame)

Method Detail

runFindMergeHaplotypes

public void runFindMergeHaplotypes(java.lang.String inFile,
                                   java.lang.String exportFile,
                                   java.lang.String errorExportFile,
                                   double maxDistance,
                                   int minSites,
                                   int appoxSitesPerHaplotype)

Produces donor haplotypes that can be used for imputation.

Parameters:

inFile - Input DNA sequence alignment file name in either HapMap or HDF5

exportFile -

errorExportFile -

maxDistance - maximum distance between founder haplotype and other haplotype

minSites -

appoxSitesPerHaplotype -

divideChromosome

public static kotlin.Array[] divideChromosome(GenotypeTable a,
                                              int appoxSitesPerHaplotype)

maxMajorAllelesTaxa

public static java.util.ArrayList<java.lang.Integer> maxMajorAllelesTaxa(GenotypeTable a,
                                                                         int numMaxTaxa,
                                                                         WHICH_ALLELE alleleNumber)

setParameters

public void setParameters(java.lang.String[] args)

performFunction

public DataSet performFunction(DataSet input)

getIcon

public javax.swing.ImageIcon getIcon()

getButtonName

public java.lang.String getButtonName()

getToolTipText

public java.lang.String getToolTipText()

main

public static void main(java.lang.String[] args)

Parameters:

args -