Package imp

Class ImpIbs

java.lang.Object

imp.ImpIbs

public final class ImpIbs
extends java.lang.Object

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

Instances of ImpIbs are immutable.

Constructor Summary

Constructors

Constructor	Description
ImpIbs(ImpData impData)	Constructs a new ImpIbs object from the specified data.

Method Summary

Modifier and Type	Method	Description
int[]	ibsHaps(int hap, int step)	Returns an array containing reference haplotype indices that that are IBS with the specified target haplotype in an interval beginning with the specified step.
ImpData	impData()	Return the data for genotype imputation in the marker window.
int	nStates()	Returns the number of HMM states per marker.
int	nSteps()	Returns the number of IBS steps in the marker window.
int	stepStart(int step)	Returns the index of the first marker in the specified step.

Methods inherited from class java.lang.Object

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

Constructor Detail

ImpIbs

public ImpIbs(ImpData impData)

Constructs a new ImpIbs object from the specified data.

Parameters:

impData - the input data for genotype imputation

Throws:

java.lang.NullPointerException - if impData == null

Method Detail

ibsHaps

public int[] ibsHaps(int hap,
                     int step)

Returns an array containing reference haplotype indices that that are IBS with the specified target haplotype in an interval beginning with the specified step. The returned array will contain fewer than this.nHapsPerStep() haplotypes if the number of reference haplotypes that are IBS with specified target haplotype in the specified step is less than this.nHapsPerStep().

Parameters:

hap - a haplotype index

step - a step index

Returns:

an array containing reference haplotype indices that that are IBS with the specified target haplotype

Throws:

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

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

impData

public ImpData impData()

Return the data for genotype imputation in the marker window.

Returns:

the data for genotype imputation in the 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 index of the first marker in the specified step.

Parameters:

step - a step index

Returns:

the index of the first marker in the specified step

Throws:

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