Package imp

Class HaplotypeCoder

java.lang.Object

imp.HaplotypeCoder

public class HaplotypeCoder
extends java.lang.Object

Class HaplotypeCoder indexes the observed allele sequences in phased reference and target genotype data in a chromosome interval.

Instances of class HaplotypeCoder are immutable.

Constructor Summary

Constructors

Constructor	Description
HaplotypeCoder(RefGT restrictRefGT, GT phasedTarg)	Constructs a new HaplotypeCoder instance from the specified data.

Method Summary

Modifier and Type	Method	Description
RefGT	refHapPairs()	Returns the phased reference genotypes at the target markers.
IndexArray	run(int start, int end)	Returns an array mapping haplotype indices to allele sequence indices in the specified marker interval.
GT	targHapPairs()	Returns the phased target genotypes.

Methods inherited from class java.lang.Object

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

Constructor Detail

HaplotypeCoder

public HaplotypeCoder(RefGT restrictRefGT,
                      GT phasedTarg)

Constructs a new HaplotypeCoder instance from the specified data.

Parameters:

restrictRefGT - the phased reference genotypes at the target markers

phasedTarg - the phased target genotypes

Throws:

java.lang.IllegalArgumentException - if refHapPairs.markers().equals(targetHapPairs.markers()) == false

java.lang.NullPointerException - if refHapPairs == null || targetHapPairs == null

Method Detail

refHapPairs

public RefGT refHapPairs()

Returns the phased reference genotypes at the target markers.

Returns:

the phased reference genotypes at the target markers

targHapPairs

public GT targHapPairs()

Returns the phased target genotypes.

Returns:

the phased target genotypes

run

public IndexArray run(int start,
                      int end)

Returns an array mapping haplotype indices to allele sequence indices in the specified marker interval. The target haplotype indices are shifted by the number of reference haplotypes in the returned array. Thus the first target haplotype index is this.refHapPairs.nHaps() and the last target haplotype index is (this.refHapPairs.nHaps() + this.targHapPairs().nHaps() - 1).

Parameters:

start - the first marker index (inclusive)

end - the last marker index (exclusive)

Returns:

an array mapping haplotype indices to allele sequence indices

Throws:

java.lang.IllegalArgumentException - if start >= end

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