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.
Modifier and Type | Method | Description |
---|---|---|
static void |
run(PhaseData phaseData,
EstPhase estPhase,
Regress recombRegress) |
Estimates and stores phased haplotypes for the target samples.
|
public static void run(PhaseData phaseData, EstPhase estPhase, Regress recombRegress)
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 distancejava.lang.IllegalArgumentException
- if nItsRemaining < 1
java.lang.NullPointerException
- if any parameter is null
or if any element of phase
is null