Package phase

Class MarkerCluster

java.lang.Object
phase.MarkerCluster
public class MarkerCluster extends Object

Class MarkerCluster represents a partition of markers into contiguous marker clusters.

Instances of class MarkerCluster are immutable.

  • Constructor Summary

    Constructors
    Constructor
    Description
    MarkerCluster(PhaseData phaseData, int sample)
    Constructs a new MarkerCluster instance from the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    clusterEnd(int index)
    Returns the exclusive end marker for the cluster.
    int
    clusterStart(int index)
    Returns the inclusive start marker for the cluster.
    boolean
    clustHasMissingGT(int index)
    Returns true if the cluster has at least one missing genotype, and returns false otherwise.
    int
    nClusters()
    Returns the number of clusters
    int
    nMissingGTClusters()
    Returns the number of clusters containing at least one missing genotype.
    FloatArray
    pRecomb()
    Return a FloatArray of size this.nClusters() whose k-th element is the probability of transitioning to a random HMM state between the k-th cluster and the previous cluster.
    IntArray
    unphClusters()
    Returns a sorted list of cluster indices in increasing order for which the cluster contains an unphased heterozygote.

    Methods inherited from class java.lang.Object

    clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

  • Constructor Details

    • MarkerCluster

      public MarkerCluster(PhaseData phaseData, int sample)
      Constructs a new MarkerCluster instance from the specified data.
      Parameters:
      phaseData - the input data for the next genotype phasing iteration
      sample - a sample index
      Throws:
      IndexOutOfBoundsException - if sample < 0 || sample >= phaseData.targGT().nSamples()
      NullPointerException - if phaseData == null

  • Method Details

    • nClusters

      public int nClusters()
      Returns the number of clusters
      Returns:
      the number of clusters

    • clusterStart

      public int clusterStart(int index)
      Returns the inclusive start marker for the cluster.
      Parameters:
      index - a cluster index
      Returns:
      the inclusive start marker for the cluster
      Throws:
      IndexOutOfBoundsException - if index < 0 || index >= this.nClusteres()

    • clusterEnd

      public int clusterEnd(int index)
      Returns the exclusive end marker for the cluster.
      Parameters:
      index - a cluster index
      Returns:
      the exclusive marker for the cluster
      Throws:
      IndexOutOfBoundsException - if index < 0 || index >= this.nClusteres()

    • pRecomb

      public FloatArray pRecomb()
      Return a FloatArray of size this.nClusters() whose k-th element is the probability of transitioning to a random HMM state between the k-th cluster and the previous cluster.
      Returns:
      a FloatArray of size this.nClusters() whose k-th element is the probability of transitioning to a random HMM state between the k-th cluster and the previous cluster

    • unphClusters

      public IntArray unphClusters()
      Returns a sorted list of cluster indices in increasing order for which the cluster contains an unphased heterozygote.
      Returns:
      a sorted list of cluster indices in increasing order for which the cluster contains an unphased heterozygote

    • clustHasMissingGT

      public boolean clustHasMissingGT(int index)
      Returns true if the cluster has at least one missing genotype, and returns false otherwise.
      Parameters:
      index - a cluster index
      Returns:
      true if the cluster has at least one missing genotype
      Throws:
      IndexOutOfBoundsException - if index < 0 || index >= this.nClusters()

    • nMissingGTClusters

      public int nMissingGTClusters()
      Returns the number of clusters containing at least one missing genotype.
      Returns:
      the number of clusters with at least one missing genotype