Package phase

Class LowFreqPhaseStates

java.lang.Object
phase.LowFreqPhaseStates
public final class LowFreqPhaseStates extends Object

Class LowFreqPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype. The resulting HMM states are enriched for reference haplotypes carrying low frequency variants.

Instances of LowFreqPhaseStates are not thread-safe.

  • Constructor Summary

    Constructors
    Constructor
    Description
    LowFreqPhaseStates(LowFreqPhaseIbs ibsHaps, int maxStates)
    Constructs a new LowFreqPhaseStates object from the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    ibsStates(int targHap, int[][] haps, byte[][] nMismatches)
    Stores the Li and Stephens HMM for the specified target haplotype in the specified arrays.
    int
    maxStates()
    Returns the maximum number of HMM states at a marker.
    int
    nMarkers()
    Returns the number of markers.
    int
    nTargHaps()
    Returns the number of target haplotypes.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • LowFreqPhaseStates

      public LowFreqPhaseStates(LowFreqPhaseIbs ibsHaps, int maxStates)
      Constructs a new LowFreqPhaseStates object from the specified data.
      Parameters:
      ibsHaps - the IBS haplotype segments
      maxStates - the maximum number of composite reference haplotypes that will be constructed
      Throws:
      IllegalArgumentException - if maxStates < 1
      NullPointerException - if ibsHaps == null

  • Method Details

    • nTargHaps

      public int nTargHaps()
      Returns the number of target haplotypes.
      Returns:
      the number of target haplotypes

    • nMarkers

      public int nMarkers()
      Returns the number of markers.
      Returns:
      the number of markers

    • maxStates

      public int maxStates()
      Returns the maximum number of HMM states at a marker.
      Returns:
      the maximum number of HMM states at a marker

    • ibsStates

      public int ibsStates(int targHap, int[][] haps, byte[][] nMismatches)
      Stores the Li and Stephens HMM for the specified target haplotype in the specified arrays. The haplotype for the j-th state at the m-th marker is stored in haps[m][j]. The number of allele mismatches (0 or 1) between the haplotype for the j-th state and the target haplotype at the m-th marker is stored in nMismatches[m][j]. The number of HMM states states at each marker is returned.
      Parameters:
      targHap - the haplotype index
      haps - the two-dimensional array in which the haplotype for each HMM state will be stored
      nMismatches - the two-dimensional array in which the number of allele mismatches (0 or 1) for each HMM state will be stored
      Returns:
      the number of HMM states at each marker
      Throws:
      IndexOutOfBoundsException - if targHap < 0 || targHap >= this.nTargHaps()
      IndexOutOfBoundsException - if haps.length < this.nMarkers()
      IndexOutOfBoundsException - if nMismatches.length < this.nMarkers()
      IndexOutOfBoundsException - if haps[m].length is less than the number of HMM states for any marker m satisfying (0 <= m && m < haps.length)
      IndexOutOfBoundsException - if nMismatches[m].length is less than the number of HMM states for any marker m satisfying (0 <= m && m < nMismatches.length)
      NullPointerException - if any array is null