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. It uses a rolling window of reference haplotypes for phasing each sample.Instances of class
PhaseLS
are not thread-safe.
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Method Summary
All Methods Static Methods Concrete Methods Modifier and Type Method Description static void
run(PhaseData phaseData, EstPhase estPhase, Regress recombRegress)
Estimates and stores phased haplotypes for the target samples.
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Method Detail
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run
public static void run(PhaseData phaseData, EstPhase estPhase, Regress recombRegress)
Estimates and stores phased haplotypes for the target samples. The returned haplotypes are ordered by increasing sample index.- Parameters:
phaseData
- the input data for an iteration of genotype phasingestPhase
- the estimated sample phaserecombRegress
- used for regression of state-switch probability on inter-marker genetic distance- Throws:
java.lang.IllegalArgumentException
- ifnItsRemaining < 1
java.lang.NullPointerException
- if any parameter isnull
or if any element ofphase
isnull
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