Package phase

Class PhaseIbs

java.lang.Object

phase.PhaseIbs

public final class PhaseIbs
extends java.lang.Object

Class PhaseIbs identifies haplotypes that share a long IBS segment with a specified haplotype.

Instances of PhaseIbs are immutable.

Constructor Summary

Constructors

Constructor	Description
PhaseIbs(PhaseData phaseData)	Constructs a new PhaseIbs object from the specified data.

Method Summary

Modifier and Type	Method	Description
IntSet	ibsHaps(int h1, int h2, int step)	Returns a set containing the specified number of haplotype indices that are IBS with haplotype h1 in the specified step.
int	nStates()	Returns the number of HMM states per marker.
int	nSteps()	Returns the number of IBS steps in the marker window.
PhaseData	phaseData()	Return the data used to phase genotypes in a marker window.
int	stepStart(int step)	Returns the first marker index in the specified step.

Methods inherited from class java.lang.Object

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

Constructor Detail

PhaseIbs

public PhaseIbs(PhaseData phaseData)

Constructs a new PhaseIbs object from the specified data.

Parameters:

phaseData - the input data for an iteration of genotype phasing

Throws:

java.lang.IllegalArgumentException - if hapPairs.markers().equals(map.markers()) == false

java.lang.IllegalArgumentException - if stepLength <= 0.0 || nStepsToMerge < 1 || nStates < 1

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

Method Detail

ibsHaps

public IntSet ibsHaps(int h1,
                      int h2,
                      int step)

Returns a set containing the specified number of haplotype indices that are IBS with haplotype h1 in the specified step. The returned set is guaranteed to not contain indices h1 or h2. The returned set will contain fewer than this.nHapsPerStep() haplotypes if the number of haplotypes that are IBS with haplotype h1 is less than this.nHapsPerStep().

Parameters:

h1 - a haplotype index

h2 - a haplotype index

step - a step index

Returns:

a set containing IBS haplotype indices

Throws:

java.lang.IndexOutOfBoundsException - if h1 < 0 || h1 >= this.hapPairs().nHaps()

java.lang.IndexOutOfBoundsException - if h2 < 0 || h2 >= this.hapPairs().nHaps()

java.lang.IndexOutOfBoundsException - if step < 0 || step >= this.nSteps()

java.lang.IllegalArgumentException - if nHaps < 0 || nHaps > (1 << 30)

phaseData

public PhaseData phaseData()

Return the data used to phase genotypes in a marker window.

Returns:

the data used to phase genotypes in a marker window

nStates

public int nStates()

Returns the number of HMM states per marker.

Returns:

the number of HMM states per marker

nSteps

public int nSteps()

Returns the number of IBS steps in the marker window.

Returns:

the number of IBS steps in the marker window

stepStart

public int stepStart(int step)

Returns the first marker index in the specified step.

Parameters:

step - a step index

Returns:

the first marker index in the specified step

Throws:

java.lang.IllegalArgumentException - if step < 0 || step >= this.nSteps()