net.maizegenetics.pangenome.hapCalling

Class PathFinderForSingleTaxonNodes

net.maizegenetics.pangenome.hapCalling.PathFinderForSingleTaxonNodes

public class PathFinderForSingleTaxonNodes

Constructor Detail

PathFinderForSingleTaxonNodes

public PathFinderForSingleTaxonNodes(@NotNull
                                     HaplotypeGraph inputGraph,
                                     @NotNull
                                     com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.HapIdSetCount> readMap,
                                     double probCorrect,
                                     double sameGameteProbability,
                                     int minReadsPerRange,
                                     int maxReadsPerKB,
                                     boolean removeEqual,
                                     double inbreedCoef,
                                     @NotNull
                                     java.lang.String parentList,
                                     boolean useLikelyParents,
                                     @Nullable
                                     MostLikelyParents parentFinder,
                                     int maxParents,
                                     double minCoverage)

Method Detail

getLikelyParents

@NotNull
public java.util.List<kotlin.Pair> getLikelyParents()

findBestPath

@NotNull
public java.util.List<net.maizegenetics.pangenome.api.HaplotypeNode> findBestPath()

findBestDiploidPath

@NotNull
public java.util.List<java.util.List> findBestDiploidPath()

getReadMap

@NotNull
public com.google.common.collect.Multimap<net.maizegenetics.pangenome.api.ReferenceRange,net.maizegenetics.pangenome.hapCalling.HapIdSetCount> getReadMap()

getProbCorrect

public double getProbCorrect()

getSameGameteProbability

public double getSameGameteProbability()

getMinReadsPerRange

public int getMinReadsPerRange()

getMaxReadsPerKB

public int getMaxReadsPerKB()

getRemoveEqual

public boolean getRemoveEqual()

getInbreedCoef

public double getInbreedCoef()