Package phase
Class PhaseLS
- java.lang.Object
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- phase.PhaseLS
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public class PhaseLS extends java.lang.Object
Class
PhaseLS
estimated genotypes phase using a haploid Li and Stephens hidden Markov model.Instances of class
PhaseLS
are immutable.
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
runStage1(PhaseData phaseData, boolean updateRecombFactor)
Estimates phased haplotypes at high-frequency markers in the target samples.static GT
runStage2(PhaseData phaseData)
Returns phased genotypes at all markers.
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Method Detail
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runStage1
public static void runStage1(PhaseData phaseData, boolean updateRecombFactor)
Estimates phased haplotypes at high-frequency markers in the target samples.- Parameters:
phaseData
- the current input data for updating genotype phase estimatesupdateRecombFactor
-true
ifphaseData.recombFactor()
should be updated- Throws:
java.lang.NullPointerException
- ifphaseData == null
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runStage2
public static GT runStage2(PhaseData phaseData)
Returns phased genotypes at all markers.- Parameters:
phaseData
- the current input data for updating genotype phase estimates- Returns:
- phased genotypes at all markers
- Throws:
java.lang.NullPointerException
- iffpd == null || phaseData == null
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