Package phase

Class CodedSteps

java.lang.Object

phase.CodedSteps

public class CodedSteps
extends java.lang.Object

Class CodedSteps divides phased genotype data into non-overlapping intervals (the steps), indexes the unique allele sequences in each interval, and stores a map of haplotype index to allele sequence index for each interval.

Constructor Summary

Constructors

Constructor	Description
CodedSteps(GT targGT, GT refGT, MarkerMap map, double step, float scaleFactor, long seed)	Constructs a new CodedSteps instance from the specified data.

Method Summary

Modifier and Type	Method	Description
IndexArray	get(int step)	Returns a map from haplotype index to allele sequence index for the specified step
int	nHaps()	Returns the number of target and reference haplotypes.
int	nMarkers()	Returns the number of markers
int	nSteps()	Returns the number of steps.
int	nTargHaps()	Returns the number of target haplotypes.
int	stepEnd(int step)	Returns the last marker index (exclusive) in the specified step.
int	stepStart(int step)	Returns the first marker index in the specified step.

Methods inherited from class java.lang.Object

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

Constructor Detail

CodedSteps

public CodedSteps(GT targGT,
                  GT refGT,
                  MarkerMap map,
                  double step,
                  float scaleFactor,
                  long seed)

Constructs a new CodedSteps instance from the specified data.

Parameters:

targGT - the phased target genotype data

refGT - the phased phased reference genotype data or null if there is no reference data

map - the genetic map

step - the step length in cM

scaleFactor - factor by which to scale the number of steps

seed - the random seed

Throws:

java.lang.IllegalArgumentException - if map.genDist().size()!=targGT.nMarkers()

java.lang.IllegalArgumentException - if refGT != null && targGT.markers().equals(refGT.markers()) == false

java.lang.IllegalArgumentException - if step <= 0.0 || Double.isFinite(step) == false

java.lang.NullPointerException - if targGT == null || map == null

Method Detail

nMarkers

public int nMarkers()

Returns the number of markers

Returns:

the number of markeres

nHaps

public int nHaps()

Returns the number of target and reference haplotypes.

Returns:

the number of target and reference haplotypes

nTargHaps

public int nTargHaps()

Returns the number of target haplotypes.

Returns:

the number of target haplotypes

nSteps

public int nSteps()

Returns the number of steps.

Returns:

the number of steps

stepStart

public int stepStart(int step)

Returns the first marker index in the specified step.

Parameters:

step - a step index

Returns:

the first marker index in the specified step

Throws:

java.lang.IllegalArgumentException - if step < 0 || step >= this.nSteps()

stepEnd

public int stepEnd(int step)

Returns the last marker index (exclusive) in the specified step.

Parameters:

step - a step index

Returns:

the lastt marker index (exclusive) in the specified step

Throws:

java.lang.IllegalArgumentException - if step < 0 || step >= this.nSteps()

get

public IndexArray get(int step)

Returns a map from haplotype index to allele sequence index for the specified step

Parameters:

step - a step index

Returns:

a map from haplotype index to allele sequence index for the specified step

Throws:

java.lang.IllegalArgumentException - if step < 0 || step >= this.nSteps()