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. It uses a rolling window of reference haplotypes for phasing each sample.

    Instances of class PhaseLS are not thread-safe.

    • Method Summary

      All Methods Static Methods Concrete Methods 
      Modifier and Type Method Description
      static void run​(PhaseData phaseData, EstPhase estPhase, Regress recombRegress)
      Estimates and stores phased haplotypes for the target samples.
      • Methods inherited from class java.lang.Object

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

      • run

        public static void run​(PhaseData phaseData,
                               EstPhase estPhase,
                               Regress recombRegress)
        Estimates and stores phased haplotypes for the target samples. The returned haplotypes are ordered by increasing sample index.
        Parameters:
        phaseData - the input data for an iteration of genotype phasing
        estPhase - the estimated sample phase
        recombRegress - used for regression of state-switch probability on inter-marker genetic distance
        Throws:
        java.lang.IllegalArgumentException - if nItsRemaining < 1
        java.lang.NullPointerException - if any parameter is null or if any element of phase is null