Package phase

Class BasicPhaseStates

java.lang.Object

phase.BasicPhaseStates

public final class BasicPhaseStates
extends java.lang.Object

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

Instances of BasicPhaseStates are not thread-safe.

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method	Description
int	ibsStates(int sample, byte[][][] nMismatches)	Stores the Li and Stephens HMM for the specified target sample in the specified arrays.
int	ibsStates(int sample, MarkerCluster mc, java.util.List<int[]> refAtMissingGT, byte[][][] nMismatches)	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.
int	nMarkers()	Returns the number of markers.
int	nTargSamples()	Returns the number of target samples.

Methods inherited from class java.lang.Object

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

Constructor Detail

BasicPhaseStates

public BasicPhaseStates(PbwtPhaseIbs ibsHaps,
                        int maxStates)

Constructs a new BasicPhaseStates 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

nTargSamples

public int nTargSamples()

Returns the number of target samples.

Returns:

the number of target samples

nMarkers

public int nMarkers()

Returns the number of markers.

Returns:

the number of markers

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,
                     MarkerCluster mc,
                     java.util.List<int[]> refAtMissingGT,
                     byte[][][] nMismatches)

Stores the Li and Stephens HMM for the specified target sample in the specified arrays. The nMismatches parameter is an array of three two-dimensional arrays: nMismatches[0] stores stores the allele mismatch data between the reference haplotypes and the haplotype composed of homozygous target genotypes, nMismatches[1] stores the allele mismatch data between the reference haplotypes and the first target haplotype, and nMismatches[2] stores the allele mismatch data between the reference haplotypes and the first target haplotype. Each two-dimensional array must have at least mc.nClusters() rows, and a column for each HMM state. An element of the two-dimensional array is 0 if the target and reference allele match and is 1 otherwise.

Parameters:

sample - the target sample index

mc - the marker clusters

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

nMismatches - arrays for storing present or absence of mismatches between target and reference alleles

Returns:

the number of state alleles at each marker

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()

java.lang.IndexOutOfBoundsException - if nMismatches.length < 3

java.lang.IndexOutOfBoundsException - if there exists j such that 0 < j && j < 3 && nMismatches[j].length < mc.nClusters()

java.lang.IndexOutOfBoundsException - if there exists j, m such that (0 < j && j < 3 && 0 < m && m < mc.nClusters()), and nMismatches[j][m].length is less than the number of model states at marker m

java.lang.IndexOutOfBoundsException - if missAlleles.get(j) is less than the number of model states for any j that indexes the missing genotypes

java.lang.NullPointerException - if (mc == null || refAtMissingGT == null) or if any array is null

ibsStates

public int ibsStates(int sample,
                     byte[][][] nMismatches)

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 nMismatchs[0][m][j] and nMismatches[1][m][j] respectively.

Parameters:

sample - the target sample index

nMismatches - an array of two two-dimensional arrays in which the number of allele mismatches with reference haplotypes for the first haplotype and the second haplotype will be stored

Returns:

the number of state alleles at each marker

Throws:

java.lang.IndexOutOfBoundsException - if sample < 0 || sample >= this.nTargSamples()

java.lang.IndexOutOfBoundsException - if nMismatches.length < 2

java.lang.IndexOutOfBoundsException - if there exists j such that (0 < j && j < 2 && nMismatches[j].length < this.nMarkers())

java.lang.IndexOutOfBoundsException - if there exists j, m such that (0 < j && j < 2 && 0 < m && m < this.nMarkers()), and nMismatches[j][m].length is less than the total number of model states

java.lang.NullPointerException - if any array is null