java.lang.Object
- vcf.SplicedGT

All Implemented Interfaces:

GT
```
public final class SplicedGT
extends java.lang.Object
implements GT
```
Class SplicedGT represents genotype emission probabilities for a set of samples. The genotype emission probabilities are determined by a RefGTWindow instance for the initial markers, and are determined by a GT instance for the remaining markers. The isPhased() and isPhased(sample) methods of the SplicedGT class return the same values as the corresponding methods of the GT instance.

Instances of class SplicedGT are immutable.

Constructor Summary

Constructors
Constructor Description

SplicedGT(GT phasedOverlap, GT gt)
Constructs a new SplicedGL instance.

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`int`	`allele(int marker, int hap)`	Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing.
`int`	`allele1(int marker, int sample)`	Returns the first allele for the specified marker and sample or return -1 if the allele is missing.
`int`	`allele2(int marker, int sample)`	Returns the second allele for the specified marker and sample or return -1 if the allele is missing.
`float`	`gl(int marker, int sample, int allele1, int allele2)`	Returns the probability of the observed data for the specified marker and sample if the specified pair of ordered alleles is the true ordered genotype.
`boolean`	`isGTData()`	Returns `true` if the value returned by `this.gl()` is determined by a called or missing genotype, and returns `false` otherwise.
`boolean`	`isPhased()`	Returns `true` if the genotype for each marker and sample is a phased, non-missing genotype, and returns `false` otherwise.
`boolean`	`isPhased(int sample)`	Returns `true` if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returns `false` otherwise.
`boolean`	`isPhased(int marker, int sample)`	Returns `true` if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returns `false` otherwise.
`Marker`	`marker(int marker)`	Returns the specified marker.
`Markers`	`markers()`	Returns the list of markers.
`int`	`nHaps()`	Returns the number of haplotypes.
`int`	`nMarkers()`	Returns the number of markers.
`int`	`nSamples()`	Returns the number of samples.
`Samples`	`samples()`	Returns the list of samples.
`java.lang.String`	`toString()`

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

- Constructor Detail
  - SplicedGT
```
public SplicedGT(GT phasedOverlap,
                 GT gt)
```
    Constructs a new SplicedGL instance.
    
    Parameters:
    
    phasedOverlap - sample haplotype pairs for the initial markers
    
    gt - genotype emission probabilities for all markers
    
    Throws:
    
    java.lang.IllegalArgumentException - if phasedOverlaps.nMarkers() >= gt.nMarkers()
    
    java.lang.IllegalArgumentException - if phasedOverlaps.marker(j).equals(gt.marker(j)) == false for any j satisfying 0 <= j && j < phasedOverlaps.nMarkers()
    
    java.lang.IllegalArgumentException - if phasedOverlaps.samples().equals(gt.samples()) == false
    
    java.lang.IllegalArgumentException - if phasedOverlap.isPhased() == false
    
    java.lang.NullPointerException - if phasedOverlap == null || gt == null
- Method Detail
  - isPhased
```
public boolean isPhased()
```
    Description copied from interface: GT
    
    Returns true if the genotype for each marker and sample is a phased, non-missing genotype, and returns false otherwise.
    
    Specified by:
    
    isPhased in interface GT
    
    Returns:
    
    true if the genotype for each marker and sample is a phased, non-missing genotype
  - isGTData
```
public boolean isGTData()
```
    Description copied from interface: GT
    
    Returns true if the value returned by this.gl() is determined by a called or missing genotype, and returns false otherwise.
    
    Specified by:
    
    isGTData in interface GT
    
    Returns:
    
    true if the value returned by this.gl() is determined by a called or missing genotype
  - isPhased
```
public boolean isPhased(int sample)
```
    Description copied from interface: GT
    
    Returns true if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returns false otherwise.
    
    Specified by:
    
    isPhased in interface GT
    
    Parameters:
    
    sample - a sample index
    
    Returns:
    
    true if the genotype for each marker for the specified sample is a phased, nonmissing genotype
  - gl
```
public float gl(int marker,
                int sample,
                int allele1,
                int allele2)
```
    Description copied from interface: GT
    
    Returns the probability of the observed data for the specified marker and sample if the specified pair of ordered alleles is the true ordered genotype.
    
    Specified by:
    
    gl in interface GT
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    allele1 - the first allele index
    
    allele2 - the second allele index
    
    Returns:
    
    the probability of the observed data for the specified marker and sample if the specified pair of ordered alleles is the true ordered genotype
  - isPhased
```
public boolean isPhased(int marker,
                        int sample)
```
    Description copied from interface: GT
    
    Returns true if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returns false otherwise.
    
    Specified by:
    
    isPhased in interface GT
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    Returns:
    
    true if the genotype for the specified marker and sample is a phased, nonmissing genotype
  - allele1
```
public int allele1(int marker,
                   int sample)
```
    Description copied from interface: GT
    
    Returns the first allele for the specified marker and sample or return -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.
    
    Specified by:
    
    allele1 in interface GT
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    Returns:
    
    the first allele for the specified marker and sample
  - allele2
```
public int allele2(int marker,
                   int sample)
```
    Description copied from interface: GT
    
    Returns the second allele for the specified marker and sample or return -1 if the allele is missing. The two alleles for a sample are arbitrarily ordered if this.unphased(marker, sample) == false.
    
    Specified by:
    
    allele2 in interface GT
    
    Parameters:
    
    marker - the marker index
    
    sample - the sample index
    
    Returns:
    
    the allele for the specified marker and sample
  - allele
```
public int allele(int marker,
                  int hap)
```
    Description copied from interface: GT
    
    Returns the allele on the specified haplotype for the specified marker or return -1 if the allele is missing. The two alleles for an individual are arbitrarily ordered if this.unphased(marker, hap/2) == false.
    
    Specified by:
    
    allele in interface GT
    
    Parameters:
    
    marker - the marker index
    
    hap - the haplotype index
    
    Returns:
    
    the allele on the specified haplotype for the specified marker
  - marker
```
public Marker marker(int marker)
```
    Description copied from interface: GT
    
    Returns the specified marker.
    
    Specified by:
    
    marker in interface GT
    
    Parameters:
    
    marker - a marker index
    
    Returns:
    
    the specified marker
  - markers
```
public Markers markers()
```
    Description copied from interface: GT
    
    Returns the list of markers.
    
    Specified by:
    
    markers in interface GT
    
    Returns:
    
    the list of markers
  - nMarkers
```
public int nMarkers()
```
    Description copied from interface: GT
    
    Returns the number of markers.
    
    Specified by:
    
    nMarkers in interface GT
    
    Returns:
    
    the number of markers
  - nHaps
```
public int nHaps()
```
    Description copied from interface: GT
    
    Returns the number of haplotypes. The returned value is equal to 2*this.nSamples().
    
    Specified by:
    
    nHaps in interface GT
    
    Returns:
    
    the number of haplotypes
  - nSamples
```
public int nSamples()
```
    Description copied from interface: GT
    
    Returns the number of samples.
    
    Specified by:
    
    nSamples in interface GT
    
    Returns:
    
    the number of samples
  - samples
```
public Samples samples()
```
    Description copied from interface: GT
    
    Returns the list of samples.
    
    Specified by:
    
    samples in interface GT
    
    Returns:
    
    the list of samples
  - toString
```
public java.lang.String toString()
```
    Overrides:
    
    toString in class java.lang.Object

Class SplicedGT

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Constructor Detail

SplicedGT

Method Detail

isPhased

isGTData

isPhased

gl

isPhased

allele1

allele2

allele

marker

markers

nMarkers

nHaps

nSamples

samples

toString