Package vcf
Class SplicedGT
- java.lang.Object
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- vcf.SplicedGT
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- All Implemented Interfaces:
GT
public final class SplicedGT extends java.lang.Object implements GT
Class
SplicedGT
represents genotypes for a set of samples that are obtained by replacing the initial markers of oneGT
instance with phased genotypes from anotherGT
instance.Instances of class
SplicedGT
are immutable.
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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.boolean
isPhased()
Returnstrue
if the genotype for each marker and sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returnsfalse
otherwise.boolean
isReversed()
Returnstrue
if the markers are ordered by decreasing chromosome base position, and returnsfalse
otherwise.Marker
marker(int marker)
Returns the specified marker.Markers
markers()
Returns the list of markers in order of increasing chromosome position.int
nHaps()
Returns the number of haplotypes.int
nMarkers()
Returns the number of markers.int
nSamples()
Returns the number of samples.GT
restrict(int start, int end)
Returns a newGT
instance restricted to genotype data for the specified markers.GT
restrict(Markers markers, int[] indices)
Returns aGT
instance restricted to genotype data for the specified markers.Samples
samples()
Returns the list of samples.java.lang.String
toString()
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Constructor Detail
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SplicedGT
public SplicedGT(GT phasedOverlap, GT gt)
Constructs a newSplicedGL
instance.- Parameters:
phasedOverlap
- sample haplotype pairs for the initial markersgt
- genotype emission probabilities for all markers- Throws:
java.lang.IllegalArgumentException
- ifphasedOverlaps.nMarkers() >= gt.nMarkers()
java.lang.IllegalArgumentException
- ifphasedOverlaps.marker(j).equals(gt.marker(j)) == false
for anyj
satisfying0 <= j && j < phasedOverlaps.nMarkers()
java.lang.IllegalArgumentException
- ifphasedOverlaps.samples().equals(gt.samples()) == false
java.lang.IllegalArgumentException
- ifphasedOverlap.isPhased() == false
java.lang.NullPointerException
- ifphasedOverlap == null || gt == null
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Method Detail
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isReversed
public boolean isReversed()
Description copied from interface:GT
Returnstrue
if the markers are ordered by decreasing chromosome base position, and returnsfalse
otherwise.- Specified by:
isReversed
in interfaceGT
- Returns:
true
if the markers are ordered by decreasing chromosome base position
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marker
public Marker marker(int marker)
Description copied from interface:GT
Returns the specified marker.
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markers
public Markers markers()
Description copied from interface:GT
Returns the list of markers in order of increasing chromosome position. If(this.isReversed() == false)
then(this.markers().marker(j).equals(this.marker(j)) == true)
for all(0 <= j && j < this.nMarkers())
. If(this.isReversed() == true)
then(this.markers().marker(this.nMarkers() - 1 - j).equals(this.marker(j)) == true)
for all(0 <= j && j < this.nMarkers())
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nMarkers
public int nMarkers()
Description copied from interface:GT
Returns the number of markers.
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nHaps
public int nHaps()
Description copied from interface:GT
Returns the number of haplotypes. The returned value is equal to2*this.nSamples()
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nSamples
public int nSamples()
Description copied from interface:GT
Returns the number of samples.
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isPhased
public boolean isPhased()
Description copied from interface:GT
Returnstrue
if the genotype for each marker and sample has non-missing alleles and is either haploid or diploid with a phased allele separator, and returnsfalse
otherwise.
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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 order of the two alleles is unspecified ifthis.isPhased() == false
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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 order of the two alleles is unspecified ifthis.isPhased() == false
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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 order of the two alleles is unspecified ifthis.isPhased() == false
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restrict
public GT restrict(Markers markers, int[] indices)
Description copied from interface:GT
Returns aGT
instance restricted to genotype data for the specified markers.
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restrict
public GT restrict(int start, int end)
Description copied from interface:GT
Returns a newGT
instance restricted to genotype data for the specified markers.
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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