Package phase
Class LowFreqPhaseIbs
- java.lang.Object
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- phase.LowFreqPhaseIbs
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- All Implemented Interfaces:
PhaseIbs
public final class LowFreqPhaseIbs extends java.lang.Object implements PhaseIbs
Class
LowFreqPhaseIbs
identifies haplotypes that share a long IBS segment or a low frequency variant with a specified haplotype in a specified genomic interval.Instances of
LowFreqPhaseIbs
are immutable.
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Constructor Summary
Constructors Constructor Description LowFreqPhaseIbs(PhaseData phaseData)
Constructs a newLowFreqPhaseIbs
object from the specified data.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
addIbsHaps(int hap, int step, PhaseStates phaseStates)
Adds haplotypes that are IBS with the specified haplotype to the HMM state space.PhaseData
phaseData()
Returns the input data for the next phase update.
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Constructor Detail
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LowFreqPhaseIbs
public LowFreqPhaseIbs(PhaseData phaseData)
Constructs a newLowFreqPhaseIbs
object from the specified data.- Parameters:
phaseData
- the current input data for updating genotype phase estimates at high-frequency markers- Throws:
java.lang.IllegalArgumentException
- iffpd.hiFreqTargGT().markers().equals(phaseData.targGT().markers()) == false
java.lang.NullPointerException
- iffpd == null || phaseData == null
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Method Detail
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phaseData
public PhaseData phaseData()
Description copied from interface:PhaseIbs
Returns the input data for the next phase update.
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addIbsHaps
public void addIbsHaps(int hap, int step, PhaseStates phaseStates)
Description copied from interface:PhaseIbs
Adds haplotypes that are IBS with the specified haplotype to the HMM state space.- Specified by:
addIbsHaps
in interfacePhaseIbs
- Parameters:
hap
- a haplotype indexstep
- an index of a genomic intervalphaseStates
- the object for constructing the HMM state space
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