main

Class HapPairSampler

java.lang.Object

main.HapPairSampler

public final class HapPairSampler
extends java.lang.Object

Class HapPairSampler samples haplotype pairs and estimates posterior genotype probabilities.

Instances of class HapPairSampler are not thread-safe.

Constructor Summary

Constructors

Constructor and Description
HapPairSampler(Par par, RunStats runStats) Constructs a new HapPairSampler instance from the specified data.

Method Summary

Modifier and Type	Method and Description
java.util.List<HapPair>	initialHaps(CurrentData cd) Returns a list of sampled haplotype pairs.
java.util.List<HapPair>	sample(CurrentData cd, java.util.List<HapPair> hapPairs, boolean useRevDag, GenotypeValues gv) Returns a list of sampled haplotype pairs.

Methods inherited from class java.lang.Object

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

Constructor Detail

HapPairSampler

public HapPairSampler(Par par,
                      RunStats runStats)

Constructs a new HapPairSampler instance from the specified data.

Parameters:

par - the analysis parameters

runStats - the object to which run-time statistics will be written

Throws:

java.lang.NullPointerException - if par == null || runStats == null

Method Detail

initialHaps

public java.util.List<HapPair> initialHaps(CurrentData cd)

Returns a list of sampled haplotype pairs. Haplotype pairs are sampled conditional on the observed genotype data and a haplotype frequency model in which all markers are in linkage equilibrium.

Parameters:

cd - the input data for the current marker window

Returns:

the a list of sampled haplotype pairs

Throws:

java.lang.NullPointerException - if cd == null

sample

public java.util.List<HapPair> sample(CurrentData cd,
                                      java.util.List<HapPair> hapPairs,
                                      boolean useRevDag,
                                      GenotypeValues gv)

Returns a list of sampled haplotype pairs. Haplotype pairs are sampled conditional on the observed genotype and a haplotype frequency model constructed from the specified hapPairs. The contract for this method is undefined if the specified hapPairs and gv are inconsistent with the input data contained in the cd parameter.

Parameters:

cd - the input data for the current marker window

hapPairs - the haplotype pairs used to build the haplotype frequency model

useRevDag - true if the order of markers should be reversed when building the haplotype frequency model, and false otherwise

gv - the current scaled genotype probabilities for the target samples or null if genotype probabilities are not to be estimated

Returns:

the sampled haplotype pairs

Throws:

java.lang.IllegalArgumentException - if haps.isEmpty() == true

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