Package phase

Class PhaseLS

java.lang.Object
phase.PhaseLS
public class PhaseLS extends Object

Class PhaseLS contains static methods for estimated genotypes phase using a haploid Li and Stephens hidden Markov model.

  • Method Details

    • runStage1

      public static void runStage1(PhaseData pd)
      Updates genotype phase estimates in the target samples.
      Parameters:
      pd - estimated phased genotypes at stage 1 markers
      Throws:
      NullPointerException - if pd == null

    • runStage2

      public static Stage2Haps runStage2(PhaseData pd)
      Returns phased genotypes at all markers.
      Parameters:
      pd - estimated phased genotypes at stage 1 markers
      Returns:
      estimated phased genotypes at all markers
      Throws:
      NullPointerException - if pd == null