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Class LiAndStephensHapSampler

java.lang.Object

main.LiAndStephensHapSampler

public final class LiAndStephensHapSampler
extends java.lang.Object

Class LiAndStephensHapSampler estimates posterior allele probabilities.

Instances of class LiAndStephensHapSampler are thread-safe.

Constructor Summary

Constructors

Constructor and Description
LiAndStephensHapSampler(Par par, GeneticMap genMap) Constructs a LiAndStephensHapSampler instance from the specified data.

Method Summary

Modifier and Type	Method and Description
BasicAlleleProbs	sample(CurrentData cd, SampleHapPairs shp) Returns estimated allele probabilities for each target sample.

Methods inherited from class java.lang.Object

clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Constructor Detail

LiAndStephensHapSampler

public LiAndStephensHapSampler(Par par,
                               GeneticMap genMap)

Constructs a LiAndStephensHapSampler instance from the specified data.

Parameters:

par - the analysis parameters

genMap - the genetic map or null if no genetic map is specified.

Throws:

java.lang.NullPointerException - if par == null

Method Detail

sample

public BasicAlleleProbs sample(CurrentData cd,
                               SampleHapPairs shp)

Returns estimated allele probabilities for each target sample. The contract for this method is undefined if the data in the specified shp and cd parameters are inconsistent.

Parameters:

cd - the input data for the current marker window

shp - estimated target haplotypes at the genotyped markers

Returns:

estimated allele probabilities for each target sample

Throws:

java.lang.NullPointerException - if cd == null || shp == null