Package phase

Class PhaseStates

java.lang.Object

phase.PhaseStates

public final class PhaseStates
extends java.lang.Object

Class PhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype or target sample.

Instances of PhaseStates are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
PhaseStates(PhaseIbs ibsHaps, int maxStates)	Constructs a new PhaseStates object from the specified data.

Method Summary

Modifier and Type	Method	Description
int	ibsStates(int targHap, int[][] haps, byte[][] nMismatches)	Stores the Li and Stephens HMM for the specified target haplotype in the specified arrays.
int	ibsStates(int sample, int[] hap1, int[] hap2, java.util.List<int[]> missAlleles, byte[][] nMismatches1, byte[][] nMismatches2)	Stores the Li and Stephens HMM for the specified target sample in the specified arrays.
int	maxStates()	Returns the maximum number of HMM states at a marker.
void	updateFields(int hap, int step)	Add the specified segment of the specified reference haplotype to the HMM state space.

Methods inherited from class java.lang.Object

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

Constructor Detail

PhaseStates

public PhaseStates(PhaseIbs ibsHaps,
                   int maxStates)

Constructs a new PhaseStates object from the specified data.

Parameters:

ibsHaps - the IBS haplotype segments

maxStates - the maximum number of composite reference haplotypes that will be constructed

Throws:

java.lang.IllegalArgumentException - if maxStates < 1

java.lang.NullPointerException - if ibsHaps == null

Method Detail

maxStates

public int maxStates()

Returns the maximum number of HMM states at a marker.

Returns:

the maximum number of HMM states at a marker

ibsStates

public int ibsStates(int sample,
                     int[] hap1,
                     int[] hap2,
                     java.util.List<int[]> missAlleles,
                     byte[][] nMismatches1,
                     byte[][] nMismatches2)

Stores the Li and Stephens HMM for the specified target sample in the specified arrays. The number of allele mismatches (0 or 1) between hap1[m] and hap2[m] for the j-th state are stored in nMismatchs1[m][j] and nMismatches2[m][j] respectively.

Parameters:

sample - the target sample index

hap1 - the alleles on the first target haplotype

hap2 - the alleles on the second target haplotype

missAlleles - a list of arrays for storing HMM state alleles at markers for which one or both target haplotypes have a missing allele

nMismatches1 - a two-dimensional array in which the number of allele mismatches (0 or 1) for hap1 for each HMM state will be stored

nMismatches2 - a two-dimensional array in which the number of allele mismatches (0 or 1) for hap2 for each HMM state will be stored

Returns:

the number of state alleles at each marker

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= phaseData.targGT().nSamples()

java.lang.IndexOutOfBoundsException - if hap1.length < this.phaseData().targGT.nMarkers()

java.lang.IndexOutOfBoundsException - if hap2.length < this.phaseData().targGT.nMarkers()

java.lang.IndexOutOfBoundsException - if nMismatches1.length < this.phaseData().targGT().nMarkers()

java.lang.IndexOutOfBoundsException - if nMismatches2.length < this.phaseData().targGT().nMarkers()

java.lang.IndexOutOfBoundsException - if missAlleles.length is less than the number of markers for which (hap1[m] < 0 || hap2[m] < 0)

java.lang.IndexOutOfBoundsException - if missAlleles.get(j) is less than the number of model states for any j satisfying (0 <= j && j < misAlleles.size())

java.lang.IndexOutOfBoundsException - if nMismatches1[m].length is less than the number of model states for any marker m satisfying (0 <= m && m < nMismatches1.length)

java.lang.IndexOutOfBoundsException - if nMismatches2[m].length is less than the number of model states for any marker m satisfying (0 <= m && m < nMismatches2.length)

java.lang.NullPointerException - if any array is null or if missAlleles == null

ibsStates

public int ibsStates(int targHap,
                     int[][] haps,
                     byte[][] nMismatches)

Stores the Li and Stephens HMM for the specified target haplotype in the specified arrays. The haplotype for the j-th state at the m-th marker is stored in haps[m][j]. The number of allele mismatches (0 or 1) between the haplotype for the j-th state and the target haplotype at the m-th marker is stored in nMismatches[m][j]. The number of HMM states states at each marker is returned.

Parameters:

targHap - the haplotype index

haps - the two-dimensional array in which the haplotype for each HMM state will be stored

nMismatches - the two-dimensional array in which the number of allele mismatches (0 or 1) for each HMM state will be stored

Returns:

the number of HMM states at each marker

Throws:

java.lang.IndexOutOfBoundsException - if targHap < 0 || targHap >= this.phaseData().targGT().nHaps()

java.lang.IndexOutOfBoundsException - if haps.length < this.phaseData.targGT().nMarkers()

java.lang.IndexOutOfBoundsException - if nMismatches.length < this.phaseData.targGT().nMarkers()

java.lang.IndexOutOfBoundsException - if haps[m].length is less than the number of model states for any marker m satisfying (0 <= m && m < haps.length)

java.lang.IndexOutOfBoundsException - if nMismatches[m].length is less than the number of model states for any marker m satisfying (0 <= m && m < nMismatches.length)

java.lang.NullPointerException - if any array is null

updateFields

public void updateFields(int hap,
                         int step)

Add the specified segment of the specified reference haplotype to the HMM state space.

Parameters:

hap - a haplotype index

step - a genomic interval

Throws:

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

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