Package imp

Class CodedSteps

java.lang.Object
imp.CodedSteps
public class CodedSteps extends Object

Class CodedSteps divides phased genotype data into non-overlapping intervals (the steps), indexes the unique allele sequences in each interval, and stores a map of haplotype index to allele sequence index for each interval.

  • Constructor Summary

    Constructors
    Constructor
    Description
    CodedSteps(ImpData impData)
    Constructs a new CodedSteps instance from the specified data.

  • Method Summary

    Modifier and Type
    Method
    Description
    IndexArray
    get(int step)
    Returns a map from haplotype index to allele sequence index for the specified step
    ImpData
    impData()
    Return the input data for genotype imputation used to construct this.
    int
    nSteps()
    Returns the number of steps.
    int
    stepStart(int step)
    Returns the first marker index in the specified step.

    Methods inherited from class java.lang.Object

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

  • Constructor Details

    • CodedSteps

      public CodedSteps(ImpData impData)
      Constructs a new CodedSteps instance from the specified data.
      Parameters:
      impData - input data for genotype imputation
      Throws:
      NullPointerException - if impData == null

  • Method Details

    • impData

      public ImpData impData()
      Return the input data for genotype imputation used to construct this.
      Returns:
      the input data for genotype imputation used to construct this

    • nSteps

      public int nSteps()
      Returns the number of steps.
      Returns:
      the number of steps

    • stepStart

      public int stepStart(int step)
      Returns the first marker index in the specified step.
      Parameters:
      step - a step index
      Returns:
      the first marker index in the specified step
      Throws:
      IllegalArgumentException - if step < 0 || step >= this.nSteps()

    • get

      public IndexArray get(int step)
      Returns a map from haplotype index to allele sequence index for the specified step
      Parameters:
      step - a step index
      Returns:
      a map from haplotype index to allele sequence index for the specified step
      Throws:
      IllegalArgumentException - if step < 0 || step >= this.nSteps()