Package phase
Class PhaseBaum1
java.lang.Object
phase.PhaseBaum1
Class PhaseBaum1
implements the forward and backward algorithms
for a haploid Li and Stephens hidden Markov model.
Instances of class PhaseBaum1
are not thread-safe.
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Constructor Summary
ConstructorsConstructorDescriptionPhaseBaum1
(PbwtPhaseIbs phaseIbs) Creates aPhaseLSBaum
instance from the specified data. -
Method Summary
Modifier and TypeMethodDescriptionstatic double
Returns the proportion of unphased heterozygotes whose phase relative to the previous heterozygote has been changed.int
Returns the number of target samples.void
phase
(int sample) Estimates and stores the phased haplotypes for the specified sample
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Constructor Details
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PhaseBaum1
Creates aPhaseLSBaum
instance from the specified data.- Parameters:
phaseIbs
- the IBS haplotype segments- Throws:
NullPointerException
- ifphaseIBS == null
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Method Details
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getAndResetSwapRate
public static double getAndResetSwapRate()Returns the proportion of unphased heterozygotes whose phase relative to the previous heterozygote has been changed. The counters for the number of heterozygotes whose phase has been changed and for the total number of heterozygotes are then re-initialized to 0.- Returns:
- the proportion of unphased heterozygotes whose phase has been changed
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nTargSamples
public int nTargSamples()Returns the number of target samples.- Returns:
- the number of target samples
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phase
public void phase(int sample) Estimates and stores the phased haplotypes for the specified sample- Parameters:
sample
- a sample index- Throws:
IndexOutOfBoundsException
- ifsample < 0 || sample >= this.nTargSamples()
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