Package phase

Class BasicPhaseStates

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

Class BasicPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype or target sample.

Instances of BasicPhaseStates are not thread-safe.

  • Constructor Summary

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

  • Method Summary

    Modifier and Type
    Method
    Description
    int
    ibsStates(int sample, byte[][][] nMismatches)
    Stores the Li and Stephens HMM for the specified target sample in the specified arrays.
    int
    ibsStates(MarkerCluster mc, List<int[]> refAtMissingGT, byte[][][] nMismatches)
    Stores the Li and Stephens HMM for the specified target sample in the specified arrays.The nMismatches parameter is an array of three two-dimensional arrays: nMismatches[0] stores stores the allele mismatch data between the reference haplotypes and the haplotype composed of homozygous target genotypes, nMismatches[1] stores the allele mismatch data between the reference haplotypes and the first target haplotype, and nMismatches[2] stores the allele mismatch data between the reference haplotypes and the first target haplotype.
    int
    maxStates()
    Returns the maximum number of HMM states at a marker.
    int
    nMarkers()
    Returns the number of markers.
    int
    nTargSamples()
    Returns the number of target samples.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • BasicPhaseStates

      public BasicPhaseStates(PbwtPhaseIbs ibsHaps, int maxStates)
      Constructs a new BasicPhaseStates 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

    • nTargSamples

      public int nTargSamples()
      Returns the number of target samples.
      Returns:
      the number of target samples

    • 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(MarkerCluster mc, List<int[]> refAtMissingGT, byte[][][] nMismatches)
      Stores the Li and Stephens HMM for the specified target sample in the specified arrays.The nMismatches parameter is an array of three two-dimensional arrays: nMismatches[0] stores stores the allele mismatch data between the reference haplotypes and the haplotype composed of homozygous target genotypes, nMismatches[1] stores the allele mismatch data between the reference haplotypes and the first target haplotype, and nMismatches[2] stores the allele mismatch data between the reference haplotypes and the first target haplotype. Each two-dimensional array must have at least mc.nClusters() rows, and a column for each HMM state. An element of the two-dimensional array is 0 if the target and reference allele match and is 1 otherwise.
      Parameters:
      mc - the marker clusters
      refAtMissingGT - a list of arrays in which HMM state alleles at markers for which one or both target haplotypes have a missing allele
      nMismatches - arrays for storing present or absence of mismatches between target and reference alleles
      Returns:
      the number of state alleles at each marker
      Throws:
      IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()
      IndexOutOfBoundsException - if nMismatches.length < 3
      IndexOutOfBoundsException - if there exists j such that 0 < j && j < 3 && nMismatches[j].length < mc.nClusters()
      IndexOutOfBoundsException - if there exists j, m such that (0 < j && j < 3 && 0 < m && m < mc.nClusters()), and nMismatches[j][m].length is less than the number of model states at marker m
      IndexOutOfBoundsException - if missAlleles.get(j) is less than the number of model states for any j that indexes the missing genotypes
      NullPointerException - if (samplePhase == null || mc == null || refAtMissingGT == null) or if any array is null

    • ibsStates

      public int ibsStates(int sample, byte[][][] nMismatches)
      Stores the Li and Stephens HMM for the specified target sample in the specified arrays. The number of allele mismatches (0 or 1) between hap1[m] and hap2[m] for the j-th state are stored in nMismatchs[0][m][j] and nMismatches[1][m][j] respectively.
      Parameters:
      sample - the target sample index
      nMismatches - an array of two two-dimensional arrays in which the number of allele mismatches with reference haplotypes for the first haplotype and the second haplotype will be stored
      Returns:
      the number of state alleles at each marker
      Throws:
      IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()
      IndexOutOfBoundsException - if nMismatches.length < 2
      IndexOutOfBoundsException - if there exists j such that (0 < j && j < 2 && nMismatches[j].length < this.nMarkers())
      IndexOutOfBoundsException - if there exists j, m such that (0 < j && j < 2 && 0 < m && m < this.nMarkers()), and nMismatches[j][m].length is less than the total number of model states
      NullPointerException - if any array is null