net.maizegenetics.analysis.imputation

Class RephaseParents

net.maizegenetics.analysis.imputation.RephaseParents

public class RephaseParents

Constructor Detail

RephaseParents

public RephaseParents()

RephaseParents

public RephaseParents(GenotypeTable originalGenotypes,
                      java.util.Map<java.lang.String,kotlin.Array[]> phasedProgeny,
                      java.util.List<kotlin.Array[]> plotList,
                      java.util.Map<java.lang.String,kotlin.Array[]> parentHapmap)

Parameters:

originalGenotypes - the GenotypeTable containing the original data being imputed

phasedProgeny - the previously imputed progeny states (0 - 4, 4 = missing)

plotList - the parentage information

parentHapmap - the parent haplotypes assigned in the previous round

RephaseParents

public RephaseParents(GenotypeTable originalGenotypes,
                      java.lang.String phasedProgeny,
                      java.lang.String parentage,
                      java.lang.String parentHaps)

Method Detail

setMinDepth

public void setMinDepth(int mindepth)

countSortOrder

public static kotlin.Array[] countSortOrder(kotlin.Array[] counts,
                                            boolean descending)

progenyStates

public static java.util.Map<java.lang.String,kotlin.Array[]> progenyStates(GenotypeTable gt)