Package phase
Interface PhaseIbs
-
- All Known Implementing Classes:
LowFreqPhaseIbs
,PbwtPhaseIbs
public interface PhaseIbs
Instances of interface
PhaseIbs
identify haplotypes that are identical by state with a specified haplotype in a specified genomic interval.All instances of
PhaseIbs
are required to be immutable.
-
-
Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description void
addIbsHaps(int hap, int step, PhaseStates phaseStates)
Adds haplotypes that are IBS with the specified haplotype to the HMM state space.PhaseData
phaseData()
Returns the input data for the next phase update.
-
-
-
Method Detail
-
phaseData
PhaseData phaseData()
Returns the input data for the next phase update.- Returns:
- the input data for the next phase update
-
addIbsHaps
void addIbsHaps(int hap, int step, PhaseStates phaseStates)
Adds haplotypes that are IBS with the specified haplotype to the HMM state space.- Parameters:
hap
- a haplotype indexstep
- an index of a genomic intervalphaseStates
- the object for constructing the HMM state space- Throws:
java.lang.IndexOutOfBoundsException
- ifhap < 0 || hap >= this.phaseData().targGT().nHaps()
java.lang.IndexOutOfBoundsException
- ifstep < 0 || step >= this.codedSteps().nSteps()
java.lang.NullPointerException
- ifphaseStates == null
-
-