Package phase
Class MarkerCluster
java.lang.Object
phase.MarkerCluster
Class MarkerCluster
represents a partition of markers into
contiguous marker clusters.
Instances of class MarkerCluster
are immutable.
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Constructor Summary
ConstructorsConstructorDescriptionMarkerCluster
(PhaseData phaseData, int sample) Constructs a newMarkerCluster
instance from the specified data. -
Method Summary
Modifier and TypeMethodDescriptionint
clusterEnd
(int index) Returns the exclusive end marker for the cluster.int
clusterStart
(int index) Returns the inclusive start marker for the cluster.boolean
clustHasMissingGT
(int index) Returnstrue
if the cluster has at least one missing genotype, and returnsfalse
otherwise.int
Returns the number of clustersint
Returns the number of clusters containing at least one missing genotype.pRecomb()
Return aFloatArray
of sizethis.nClusters()
whosek
-th element is the probability of transitioning to a random HMM state between thek
-th cluster and the previous cluster.Returns a sorted list of cluster indices in increasing order for which the cluster contains an unphased heterozygote.
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Constructor Details
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MarkerCluster
Constructs a newMarkerCluster
instance from the specified data.- Parameters:
phaseData
- the input data for the next genotype phasing iterationsample
- a sample index- Throws:
IndexOutOfBoundsException
- ifsample < 0 || sample >= phaseData.targGT().nSamples()
NullPointerException
- ifphaseData == null
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Method Details
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nClusters
public int nClusters()Returns the number of clusters- Returns:
- the number of clusters
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clusterStart
public int clusterStart(int index) Returns the inclusive start marker for the cluster.- Parameters:
index
- a cluster index- Returns:
- the inclusive start marker for the cluster
- Throws:
IndexOutOfBoundsException
- ifindex < 0 || index >= this.nClusteres()
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clusterEnd
public int clusterEnd(int index) Returns the exclusive end marker for the cluster.- Parameters:
index
- a cluster index- Returns:
- the exclusive marker for the cluster
- Throws:
IndexOutOfBoundsException
- ifindex < 0 || index >= this.nClusteres()
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pRecomb
Return aFloatArray
of sizethis.nClusters()
whosek
-th element is the probability of transitioning to a random HMM state between thek
-th cluster and the previous cluster.- Returns:
- a
FloatArray
of sizethis.nClusters()
whosek
-th element is the probability of transitioning to a random HMM state between thek
-th cluster and the previous cluster
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unphClusters
Returns a sorted list of cluster indices in increasing order for which the cluster contains an unphased heterozygote.- Returns:
- a sorted list of cluster indices in increasing order for which the cluster contains an unphased heterozygote
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clustHasMissingGT
public boolean clustHasMissingGT(int index) Returnstrue
if the cluster has at least one missing genotype, and returnsfalse
otherwise.- Parameters:
index
- a cluster index- Returns:
true
if the cluster has at least one missing genotype- Throws:
IndexOutOfBoundsException
- ifindex < 0 || index >= this.nClusters()
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nMissingGTClusters
public int nMissingGTClusters()Returns the number of clusters containing at least one missing genotype.- Returns:
- the number of clusters with at least one missing genotype
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