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 and Description |
---|
RecombHapPairSampler(Par par,
RunStats runStats)
Constructs a new
RecombHapPairSampler instance from the
specified data. |
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.
|
public RecombHapPairSampler(Par par, RunStats runStats)
RecombHapPairSampler
instance from the
specified data.par
- the analysis parametersrunStats
- the object to which run-time statistics will be writtenjava.lang.NullPointerException
- if
par == null || runStats == null
public java.util.List<HapPair> sample(CurrentData cd, java.util.List<HapPair> hapPairs, boolean useRevDag, GenotypeValues gv)
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.cd
- the input data for the current marker windowhapPairs
- the target haplotype pairs used to build the haplotype
frequency modeluseRevDag
- true
if the order of markers should
be reversed when building the haplotype frequency model, and
false
otherwisegv
- the current scaled genotype probabilities for the target
samples or null
if genotype probabilities are not to be estimatedjava.lang.IllegalArgumentException
- if haps.isEmpty() == true
java.lang.NullPointerException
- if cd == null || hapPairs == null