Package phase
Class PbwtPhaseIbs
- java.lang.Object
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- phase.PbwtPhaseIbs
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- All Implemented Interfaces:
PhaseIbs
public final class PbwtPhaseIbs extends java.lang.Object implements PhaseIbs
Class
PbwtPhaseIBS
uses the Positional Burrows-Wheeler Transform (PBWT) to find long IBS haplotypes for each sample that contain a specified small genomic interval.Instances of class
PBWT
are thread-safe.Reference: Durbin, R. 2014. Bioinformatics 30(9):1266–1272. doi:10.1093/bioinformatics/btu014
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Constructor Summary
Constructors Constructor Description PbwtPhaseIbs(PhaseData phaseData, boolean useBwd)
Constructs a newPbwtPhaseIBS
instance 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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PbwtPhaseIbs
public PbwtPhaseIbs(PhaseData phaseData, boolean useBwd)
Constructs a newPbwtPhaseIBS
instance from the specified data.- Parameters:
phaseData
- the current input data for genotype phasinguseBwd
-true
if reverse order PBWT should be used- Throws:
java.lang.NullPointerException
- ifphaseData == 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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