net.maizegenetics.analysis.imputation

Class ImputationUtils

net.maizegenetics.analysis.imputation.ImputationUtils

public class ImputationUtils

Field Detail

tab

public static java.util.regex.Pattern tab

Method Detail

main

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

order

public static kotlin.Array[] order(kotlin.Array[] array)

reverseOrder

public static kotlin.Array[] reverseOrder(kotlin.Array[] array)

getTwoClusters

public static GenotypeTable[] getTwoClusters(GenotypeTable gt,
                                             kotlin.Array[] parentIndex)

getTwoClusters

public static GenotypeTable[] getTwoClusters(GenotypeTable inputAlignment,
                                             int minGametesPerTaxon)

snpsAsFloatVector

public static kotlin.Array[] snpsAsFloatVector(BitSet[] alleles,
                                               int nsnps)

getManhattanDistance

public static float getManhattanDistance(kotlin.Array[] loc,
                                         kotlin.Array[] t,
                                         int nsnps)

getMeanLocation

public static kotlin.Array[] getMeanLocation(kotlin.Array[] loc,
                                             kotlin.Array[] size,
                                             kotlin.Array[] t,
                                             boolean add,
                                             int nsnps)

getMeanLocation

public static kotlin.Array[] getMeanLocation(kotlin.Array[] locs)

printAlleleStats

public static void printAlleleStats(GenotypeTable gt,
                                    java.lang.String name)

mergeNonconsensusFiles

public static void mergeNonconsensusFiles(java.lang.String dir,
                                          java.lang.String match,
                                          java.lang.String outfileName)

filterFiles

public static java.io.File[] filterFiles(java.lang.String dir,
                                         java.lang.String match)

mergeFiles

public static void mergeFiles(java.io.File[] mergeFiles,
                              int idcol,
                              int datacol,
                              kotlin.Array[] colOrder,
                              java.lang.String outfile)

imputeLinkageMarkers

public static void imputeLinkageMarkers(double interval,
                                        boolean hapmapFormat,
                                        java.lang.String origsnpFile,
                                        java.lang.String snpfilePattern,
                                        java.lang.String outfilePattern)

imputeLinkageMarkersAcrossFamilies

public static void imputeLinkageMarkersAcrossFamilies(double interval,
                                                      boolean hapmapFormat,
                                                      boolean excludeTaxa)

useTaxon

public static boolean useTaxon(java.lang.String name,
                               java.util.LinkedList<java.lang.String> excludelist)

isB73HaplotypeA

public static boolean isB73HaplotypeA(GenotypeTable a)

imputeLinkageMarkersFrom1106

public static void imputeLinkageMarkersFrom1106(double interval)

getListOfTaxa

public static java.util.LinkedList<java.lang.String> getListOfTaxa(java.lang.String filename)

serializePhasedHaplotypes

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

restorePhasedHaplotypes

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

exportCrossoverPositions

public static void exportCrossoverPositions(java.lang.String parentcallFilename,
                                            java.lang.String outputFilename)

exportCrossoverPositionsByParent

public static void exportCrossoverPositionsByParent(java.lang.String parentcallFilename,
                                                    java.lang.String outputMomFilename,
                                                    java.lang.String outputDadFilename)