Package phase

Class PhaseLS

java.lang.Object

phase.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

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