net.maizegenetics.pangenome.hapCalling

Class PathFinderForSingleTaxonNodesFactory

net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodesFactory

public class PathFinderForSingleTaxonNodesFactory

Constructor Detail

PathFinderForSingleTaxonNodesFactory

public PathFinderForSingleTaxonNodesFactory(@NotNull
                                            HaplotypeGraph graph,
                                            double sameGameteProbability,
                                            @Nullable
                                            net.maizegenetics.taxa.TaxaList requiredTaxaList,
                                            double probCorrect,
                                            int minTaxaPerRange,
                                            int minReadsPerRange,
                                            int maxReadsPerKB,
                                            boolean removeEqual,
                                            double inbreedCoef,
                                            int maxParents,
                                            double minCoverage)

Method Detail

getMyGraph

@NotNull
public HaplotypeGraph getMyGraph()

getUseLikelyParents

public boolean getUseLikelyParents()

getParentFinder

@Nullable
public MostLikelyParents getParentFinder()

build

@NotNull
public PathFinderForSingleTaxonNodes build(@NotNull
                                                    com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.HapIdSetCount> readMap,
                                                    @NotNull
                                                    java.lang.String parentList)

getSameGameteProbability

public double getSameGameteProbability()

getRequiredTaxaList

@Nullable
public net.maizegenetics.taxa.TaxaList getRequiredTaxaList()

getProbCorrect

public double getProbCorrect()

getMinTaxaPerRange

public int getMinTaxaPerRange()

getMinReadsPerRange

public int getMinReadsPerRange()

getMaxReadsPerKB

public int getMaxReadsPerKB()

getRemoveEqual

public boolean getRemoveEqual()

getInbreedCoef

public double getInbreedCoef()

getMaxParents

public int getMaxParents()

getMinCoverage

public double getMinCoverage()