Package phase
Class PbwtIbsData
java.lang.Object
phase.PbwtIbsData
Class PbwtIbsData
contains parameters and data for finding
haplotypes that share an IBS segment with a target haplotype.
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Constructor Summary
ConstructorsConstructorDescriptionPbwtIbsData
(PhaseData phaseData, CodedSteps codedSteps) Constructs a newPbwtIbsData
instance from the specified data. -
Method Summary
Modifier and TypeMethodDescriptionReturns the coded steps.int
Returns the number of backoff stepsint
nBatches()
Returns the number of batches.int
Returns the number of candidate haplotypesint
nHaps()
Returns the total number of target and reference haplotypes.int
Returns the number of overlap stepsint
Returns the number of target haplotypes.int
Returns the number of steps per batch
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Constructor Details
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PbwtIbsData
Constructs a newPbwtIbsData
instance from the specified data.- Parameters:
phaseData
- the current genotype phase estimates and parameter valuescodedSteps
- the coded steps- Throws:
IllegalArgumentException
- ifphaseData.fpd().stage1Steps() != codedSteps.steps()
IllegalArgumentException
- ifphaseData.fpd().stage1XRefGT()!=codedSteps.refHaps()
IllegalArgumentException
- ifphaseData.fpd().targGT().samples()!=codedSteps.targSamples()
NullPointerException
- ifphaseData == null || codedSteps == null
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Method Details
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codedSteps
Returns the coded steps.- Returns:
- the codedSteps
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nHaps
public int nHaps()Returns the total number of target and reference haplotypes.- Returns:
- the total number of target and reference haplotypes
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nTargHaps
public int nTargHaps()Returns the number of target haplotypes.- Returns:
- the number of target haplotypes
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nCandidates
public int nCandidates()Returns the number of candidate haplotypes- Returns:
- the number of candidate haploytpes
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nOverlapSteps
public int nOverlapSteps()Returns the number of overlap steps- Returns:
- the number of overlap steps
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maxBackoffSteps
public int maxBackoffSteps()Returns the number of backoff steps- Returns:
- the number of backoff steps
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stepsPerBatch
public int stepsPerBatch()Returns the number of steps per batch- Returns:
- the number of steps per batch
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nBatches
public int nBatches()Returns the number of batches.- Returns:
- the number of batches
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