Package phase

Class SamplePhase

java.lang.Object

phase.SamplePhase

public final class SamplePhase
extends java.lang.Object

Each instance of class SamplePhase stores an estimated haplotype pair for a sample, the list of markers with missing genotypes for the sample, a list of markers whose genotype phase with respect to the preceding heterozygote genotype is considered to be uncertain for the sample, and a set of marker clusters for the sample.

Instances of class SamplePhase are not thread-safe.

Constructor Summary

Constructors

Constructor	Description
SamplePhase(Markers markers, DoubleArray genPos, int[] hap1, int[] hap2, IntArray unphased, IntArray missing)	Constructs a new SamplePhase instance from the specified data.

Method Summary

Modifier and Type	Method	Description
int	allele1(int marker)	Returns the allele on the first haplotype for the specified marker.
int	allele2(int marker)	Returns the allele on the second haplotype for the specified marker.
int[]	clustEnds()	Returns the (exclusive) end marker indices of each marker cluster.
void	getHaps(BitArray hap1, BitArray hap2)	Copies the stored haplotypes to the specified BitList objects
BitArray	hap1()	Returns the first haplotype.
BitArray	hap2()	Returns the second haplotype.
Markers	markers()	Returns the list of markers.
IntArray	missing()	Returns a list of marker indices in increasing order for which the genotype is missing.
void	setAllele1(int marker, int allele)	Sets the allele on the first haplotype for the specified marker to the specified allele
void	setAllele2(int marker, int allele)	Sets the allele on the second haplotype for the specified marker to the specified allele
void	setUnphased(IntArray unphased)	Sets the list of markers whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.
void	swapHaps(int start, int end)	Swaps the alleles of the two haplotypes in the specified range of markers.
static BitArray[]	toBitLists(EstPhase estPhase)	Returns the current estimated phased genotypes.
IntArray	unphased()	Returns a list of marker indices in increasing order whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.

Methods inherited from class java.lang.Object

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

Constructor Detail

SamplePhase

public SamplePhase(Markers markers,
                   DoubleArray genPos,
                   int[] hap1,
                   int[] hap2,
                   IntArray unphased,
                   IntArray missing)

Constructs a new SamplePhase instance from the specified data.

Parameters:

markers - the list of markers

genPos - the genetic positions of the specifed markers

hap1 - the list of alleles on the first haplotype

hap2 - the list of alleles on the second haplotype

unphased - the indices of markers whose genotype phase with respect to the preceding heterozygote is unknown

missing - the indices of markers whose genotype is missing

Throws:

java.lang.IllegalArgumentException - if genPos.size() != markers.nMarkers()

java.lang.IllegalArgumentException - if hap1.length != markers.nMarkers() || hap2.length != markers.nMarkers()

java.lang.IllegalArgumentException - if the specified unphased or missing list is not a strictly increasing list of marker indices between 0 (inclusive) and markers.nMarkers() (exclusive)

java.lang.NullPointerException - if any argument is null

Method Detail

clustEnds

public int[] clustEnds()

Returns the (exclusive) end marker indices of each marker cluster. The returned list is sorted in increasing order.

Returns:

the (exclusive) end marker indices of each marker cluster

markers

public Markers markers()

Returns the list of markers.

Returns:

the list of markers

missing

public IntArray missing()

Returns a list of marker indices in increasing order for which the genotype is missing.

Returns:

a list of marker indices in increasing order for which the genotype is missing

unphased

public IntArray unphased()

Returns a list of marker indices in increasing order whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.

Returns:

a list of markers indices in increasing order whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown

setUnphased

public void setUnphased(IntArray unphased)

Sets the list of markers whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown.

Parameters:

unphased - a list of markers whose genotype phase with respect to the preceding non-missing heterozygote genotype is unknown

Throws:

java.lang.IllegalArgumentException - if the specified list or marker indices is not a strictly increasing list of indices between 0 (inclusive) and this.markers().nMarkers() (exclusive)

java.lang.NullPointerException - if unphased == null

getHaps

public void getHaps(BitArray hap1,
                    BitArray hap2)

Copies the stored haplotypes to the specified BitList objects

Parameters:

hap1 - a BitList in which the sample's first haplotype's alleles will be stored

hap2 - a BitList in which the sample's second haplotype's alleles will be stored

Throws:

java.lang.IllegalArgumentException - if hap1.size() != this.markers().sumHaplotypeBits()

java.lang.IllegalArgumentException - if hap2.size()!= this.markers().sumHaplotypeBits()

java.lang.NullPointerException - if hap1 == null || hap2 == null

allele1

public int allele1(int marker)

Returns the allele on the first haplotype for the specified marker.

Parameters:

marker - the marker index

Returns:

the allele on the first haplotype for the specified marker

Throws:

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

allele2

public int allele2(int marker)

Returns the allele on the second haplotype for the specified marker.

Parameters:

marker - the marker index

Returns:

the allele on the second haplotype for the specified marker

Throws:

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

setAllele1

public void setAllele1(int marker,
                       int allele)

Sets the allele on the first haplotype for the specified marker to the specified allele

Parameters:

marker - the marker index

allele - the allele

Throws:

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

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

setAllele2

public void setAllele2(int marker,
                       int allele)

Sets the allele on the second haplotype for the specified marker to the specified allele

Parameters:

marker - the marker index

allele - the allele

Throws:

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

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

swapHaps

public void swapHaps(int start,
                     int end)

Swaps the alleles of the two haplotypes in the specified range of markers.

Parameters:

start - the start marker index (inclusive)

end - the end marker index (exclusive)

Throws:

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

hap1

public BitArray hap1()

Returns the first haplotype. The haplotype is encoded with the this.markers().allelesToBits() method.

Returns:

the first haplotype

hap2

public BitArray hap2()

Returns the second haplotype. The haplotype is encoded with the this.markers().allelesToBits() method.

Returns:

the second haplotype

toBitLists

public static BitArray[] toBitLists(EstPhase estPhase)

Returns the current estimated phased genotypes. This method converts column-major data into row-major data.

Parameters:

estPhase - the current estimated phased genotypes for each target sample

Returns:

the current estimated phased genotypes

Throws:

java.lang.NullPointerException - if estPhase == null