Package phase

Class HapImputer

java.lang.Object

phase.HapImputer

public class HapImputer
extends java.lang.Object

Class ImputableHaps performs imputation to estimate missing alleles and missing haplotype phase.

Instances of ImputableHaps are thread-safe.

Constructor Summary

Constructors

Constructor	Description
HapImputer(Markers markers, Samples samples)	Constructs a new ImputedHaps instance from the specified data.

Method Summary

Modifier and Type	Method	Description
GT	imputedHaps()	Returns the imputed haplotypes.
Markers	markers()	Returns the list of markers.
void	setHap(int hap, int[] alleles)	Stores the specified haplotype.
void	setPartlyImputedAllele(int hap, int marker, float[] alProbs, IntList refHaps, FloatList stateProbs)	Stores a partially-imputed allele.
Samples	targSamples()	Returns the list of target samples.

Methods inherited from class java.lang.Object

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

Constructor Detail

HapImputer

public HapImputer(Markers markers,
                  Samples samples)

Constructs a new ImputedHaps instance from the specified data.

Parameters:

markers - the list of markers

samples - the list of target samples

Throws:

java.lang.NullPointerException - if markers == null || samples == null

Method Detail

targSamples

public Samples targSamples()

Returns the list of target samples.

Returns:

the list of target samples

markers

public Markers markers()

Returns the list of markers.

Returns:

the list of markers

setHap

public void setHap(int hap,
                   int[] alleles)

Stores the specified haplotype.

Parameters:

hap - the haplotype index

alleles - the haplotype

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= 2*this.samples()

java.lang.IllegalArgumentException - if alleles.length != this.markers().nMarkers()

java.lang.NullPointerException - if alleles == null

setPartlyImputedAllele

public void setPartlyImputedAllele(int hap,
                                   int marker,
                                   float[] alProbs,
                                   IntList refHaps,
                                   FloatList stateProbs)

Stores a partially-imputed allele. if alProbs.length < this.markers().marker(marker).nAlleles(), the missing allele probabilities are assumed to be 0.0.

Parameters:

hap - the haplotype index

marker - the marker index

alProbs - the posterior allele probabilities computed from a subset of HMM states

refHaps - the list of reference haplotypes for HMM states not included in the specified allele probabilities

stateProbs - the list of state probabilities for each HMM state in the specified list of reference haplotypes

Throws:

java.lang.IndexOutOfBoundsException - if hap < 0 || hap >= 2 * this.targSamples().nSamples()

java.lang.IndexOutOfBoundsException - if marker < 0 || marker >= this.markers().nMarkers()

java.lang.IllegalArgumentException - if refHaps.size() != stateProbs.size()

java.lang.NullPointerException - if alProbs == null || refHaps == null || stateProbs == null

imputedHaps

public GT imputedHaps()

Returns the imputed haplotypes.

Returns:

the imputed haplotypes

Throws:

java.lang.NullPointerException - if this.setHap() has not previously been called for each haplotype h satisfying (0 <= h && h <= 2 * this.targSamples().nSamples())