Package phase

Class PhaseLS


  • public class PhaseLS
    extends java.lang.Object

    Class PhaseLS estimated genotypes phase using a haploid Li and Stephens hidden Markov model.

    Instances of class PhaseLS are immutable.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void runStage1​(PhaseData phaseData, boolean updateRecombFactor)
      Estimates phased haplotypes at high-frequency markers in the target samples.
      static GT runStage2​(PhaseData phaseData)
      Returns phased genotypes at all markers.
      • Methods inherited from class java.lang.Object

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

      • runStage1

        public static void runStage1​(PhaseData phaseData,
                                     boolean updateRecombFactor)
        Estimates phased haplotypes at high-frequency markers in the target samples.
        Parameters:
        phaseData - the current input data for updating genotype phase estimates
        updateRecombFactor - true if phaseData.recombFactor() should be updated
        Throws:
        java.lang.NullPointerException - if phaseData == null
      • runStage2

        public static GT runStage2​(PhaseData phaseData)
        Returns phased genotypes at all markers.
        Parameters:
        phaseData - the current input data for updating genotype phase estimates
        Returns:
        phased genotypes at all markers
        Throws:
        java.lang.NullPointerException - if fpd == null || phaseData == null