main

Class RecombHapPairSampler

java.lang.Object

main.RecombHapPairSampler

public class RecombHapPairSampler
extends java.lang.Object

Class RecombHapPairSamples samples haplotype pairs and estimates posterior genotype probabilities using a haplotype frequency model that permits transitions between any two states at adjacent markers.

Instances of class RecombHapPairSampler are not thread-safe.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
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

RecombHapPairSampler

public RecombHapPairSampler(Par par,
                            RunStats runStats)

Constructs a new RecombHapPairSampler 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

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 target 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