net.maizegenetics.analysis.imputation

Class SelfedHaplotypeFinder

net.maizegenetics.analysis.imputation.SelfedHaplotypeFinder

public class SelfedHaplotypeFinder

Constructor Detail

SelfedHaplotypeFinder

public SelfedHaplotypeFinder(int window,
                             double minProportionNotMissing)

Method Detail

main

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

phaseSelfedParents

public java.util.Map<java.lang.String,kotlin.Array[]> phaseSelfedParents(java.nio.file.Path parentpath,
                                                                         java.nio.file.Path savepath)

clusterWindow

public HaplotypeClusterer clusterWindow(GenotypeTable a,
                                        int start,
                                        int length,
                                        int maxdif,
                                        int minNotMissingPerHaplotype)

serializePhasedHaplotypes

public static void serializePhasedHaplotypes(java.util.Map<java.lang.String,kotlin.Array[]> phasedHaps,
                                             java.nio.file.Path savePath)

restorePhasedHaplotypes

public static java.util.Map<java.lang.String,kotlin.Array[]> restorePhasedHaplotypes(java.nio.file.Path restorePath)

setGenotype

public void setGenotype(GenotypeTable genotype)

correctSelfPhaseUsingCross

public void correctSelfPhaseUsingCross(java.lang.String selfPhaseFilename,
                                       java.lang.String crossPhaseFilename,
                                       java.lang.String parent,
                                       int chr,
                                       java.lang.String outfileName)