Package phase

Class LowFreqPhaseStates

java.lang.Object

phase.LowFreqPhaseStates

public final class LowFreqPhaseStates
extends java.lang.Object

Class LowFreqPhaseStates has methods for constructing a Li and Stephens HMM for a target haplotype. The resulting HMM states are enriched for reference haplotypes carrying low frequency variants.

Instances of LowFreqPhaseStates are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
LowFreqPhaseStates(LowFreqPhaseIbs ibsHaps, int maxStates)	Constructs a new LowFreqPhaseStates 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	maxStates()	Returns the maximum number of HMM states at a marker.
int	nMarkers()	Returns the number of markers.
int	nTargHaps()	Returns the number of target haplotypes.

Methods inherited from class java.lang.Object

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

Constructor Detail

LowFreqPhaseStates

public LowFreqPhaseStates(LowFreqPhaseIbs ibsHaps,
                          int maxStates)

Constructs a new LowFreqPhaseStates 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

nTargHaps

public int nTargHaps()

Returns the number of target haplotypes.

Returns:

the number of target haplotypes

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 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.nTargHaps()

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

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

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

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

java.lang.NullPointerException - if any array is null