Package phase

Class PbwtIbsData

java.lang.Object
phase.PbwtIbsData

public class PbwtIbsData extends Object

Class PbwtIbsData contains parameters and data for finding haplotypes that share an IBS segment with a target haplotype.

  • Constructor Details

    • PbwtIbsData

      public PbwtIbsData(PhaseData phaseData, CodedSteps codedSteps)
      Constructs a new PbwtIbsData instance from the specified data.
      Parameters:
      phaseData - the current genotype phase estimates and parameter values
      codedSteps - the coded steps
      Throws:
      IllegalArgumentException - if phaseData.fpd().stage1Steps() != codedSteps.steps()
      IllegalArgumentException - if phaseData.fpd().stage1XRefGT()!=codedSteps.refHaps()
      IllegalArgumentException - if phaseData.fpd().targGT().samples()!=codedSteps.targSamples()
      NullPointerException - if phaseData == null || codedSteps == null
  • Method Details

    • codedSteps

      public CodedSteps codedSteps()
      Returns the coded steps.
      Returns:
      the codedSteps
    • nHaps

      public int nHaps()
      Returns the total number of target and reference haplotypes.
      Returns:
      the total number of target and reference haplotypes
    • nTargHaps

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

      public int nCandidates()
      Returns the number of candidate haplotypes
      Returns:
      the number of candidate haploytpes
    • nOverlapSteps

      public int nOverlapSteps()
      Returns the number of overlap steps
      Returns:
      the number of overlap steps
    • maxBackoffSteps

      public int maxBackoffSteps()
      Returns the number of backoff steps
      Returns:
      the number of backoff steps
    • stepsPerBatch

      public int stepsPerBatch()
      Returns the number of steps per batch
      Returns:
      the number of steps per batch
    • nBatches

      public int nBatches()
      Returns the number of batches.
      Returns:
      the number of batches