Package phase

Class ImputeBaum


  • public class ImputeBaum
    extends java.lang.Object

    Class ImputeBaum applies the forward and backward algorithms for a haploid Li and Stephens hidden Markov model at high-frequency markers, and imputes missing genotypes and heterozygote phase at low-frequency markers.

    Instances of class ImputeBaum are not thread-safe.

    • Constructor Summary

      Constructors 
      Constructor Description
      ImputeBaum​(PhaseIbs phaseIbs, HapImputer hapImputer)
      Creates a ImputeBaum instance from the specified data.
    • Method Summary

      All Methods Instance Methods Concrete Methods 
      Modifier and Type Method Description
      int nTargSamples()
      Returns the number of target samples.
      void phase​(int sample)
      Estimates phased haplotypes for the specified sample.
      • Methods inherited from class java.lang.Object

        clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
    • Constructor Detail

      • ImputeBaum

        public ImputeBaum​(PhaseIbs phaseIbs,
                          HapImputer hapImputer)
        Creates a ImputeBaum instance from the specified data.
        Parameters:
        phaseIbs - the IBS haplotypes
        hapImputer - an object for imputing haplotypes at low-frequency markers
        Throws:
        java.lang.NullPointerException - if phaseIbs == null || hapImputer == null
    • Method Detail

      • nTargSamples

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

        public void phase​(int sample)
        Estimates phased haplotypes for the specified sample.
        Parameters:
        sample - a sample index
        Throws:
        java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()