Package vcf
Interface GT
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- All Known Subinterfaces:
RefGT
- All Known Implementing Classes:
BasicGT
,BasicRefGT
,EstPhase.HapsGT
,HapPairPhasedGT
,SplicedGT
,XBasicGT
public interface GT
Interface
GT
represents genotype data for a list of markers and a list of samples.All instances of
GT
are required to be immutable.
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Method Summary
All Methods Instance Methods Abstract Methods Default 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.default 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.default boolean
isGTData()
Returnstrue
if the value returned bythis.gl()
is determined by a called or missing genotype, and returnsfalse
otherwise.boolean
isPhased()
Returnstrue
if the genotype for each marker and sample is a phased, non-missing genotype, and returnsfalse
otherwise.boolean
isPhased(int sample)
Returnstrue
if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returnsfalse
otherwise.boolean
isPhased(int marker, int sample)
Returnstrue
if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returnsfalse
otherwise.Marker
marker(int marker)
Returns the specified marker.Markers
markers()
Returns the list of markers.default 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.
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Method Detail
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nMarkers
int nMarkers()
Returns the number of markers.- Returns:
- the number of markers
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markers
Markers markers()
Returns the list of markers.- Returns:
- the list of markers
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marker
Marker marker(int marker)
Returns the specified marker.- Parameters:
marker
- a marker index- Returns:
- the specified marker
- Throws:
java.lang.IndexOutOfBoundsException
- ifmarker < 0 || marker >= this.nMarkers()
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nHaps
default int nHaps()
Returns the number of haplotypes. The returned value is equal to2*this.nSamples()
.- Returns:
- the number of haplotypes
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nSamples
int nSamples()
Returns the number of samples.- Returns:
- the number of samples
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samples
Samples samples()
Returns the list of samples.- Returns:
- the list of samples
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allele1
int allele1(int marker, int sample)
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 ifthis.unphased(marker, sample) == false
.- Parameters:
marker
- the marker indexsample
- the sample index- Returns:
- the first allele for the specified marker and sample
- Throws:
java.lang.IndexOutOfBoundsException
- ifmarker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- ifsample < 0 || sample >= this.nSamples()
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allele2
int allele2(int marker, int sample)
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 ifthis.unphased(marker, sample) == false
.- Parameters:
marker
- the marker indexsample
- the sample index- Returns:
- the allele for the specified marker and sample
- Throws:
java.lang.IndexOutOfBoundsException
- ifmarker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- ifsample < 0 || sample >= this.nSamples()
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allele
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. The two alleles for an individual are arbitrarily ordered ifthis.unphased(marker, hap/2) == false
.- Parameters:
marker
- the marker indexhap
- the haplotype index- Returns:
- the allele on the specified haplotype for the specified marker
- Throws:
java.lang.IndexOutOfBoundsException
- ifmarker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- ifhap < 0 || hap >= this.nHaps()
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isPhased
boolean isPhased(int marker, int sample)
Returnstrue
if the genotype for the specified marker and sample is a phased, nonmissing genotype, and returnsfalse
otherwise.- Parameters:
marker
- the marker indexsample
- the sample index- Returns:
true
if the genotype for the specified marker and sample is a phased, nonmissing genotype- Throws:
java.lang.IndexOutOfBoundsException
- ifmarker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- ifsample < 0 || sample >= this.nSamples()
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isPhased
boolean isPhased(int sample)
Returnstrue
if the genotype for each marker for the specified sample is a phased, nonmissing genotype, and returnsfalse
otherwise.- Parameters:
sample
- a sample index- Returns:
true
if the genotype for each marker for the specified sample is a phased, nonmissing genotype- Throws:
java.lang.IndexOutOfBoundsException
- ifsample < 0 || sample >= this.nSamples()
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isPhased
boolean isPhased()
Returnstrue
if the genotype for each marker and sample is a phased, non-missing genotype, and returnsfalse
otherwise.- Returns:
true
if the genotype for each marker and sample is a phased, non-missing genotype
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isGTData
default boolean isGTData()
Returnstrue
if the value returned bythis.gl()
is determined by a called or missing genotype, and returnsfalse
otherwise.- Returns:
true
if the value returned bythis.gl()
is determined by a called or missing genotype
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gl
default 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.- Parameters:
marker
- the marker indexsample
- the sample indexallele1
- the first allele indexallele2
- 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
- Throws:
java.lang.IndexOutOfBoundsException
- ifmarker < 0 || marker >= this.nMarkers()
java.lang.IndexOutOfBoundsException
- ifsamples < 0 || samples >= this.nSamples()
java.lang.IndexOutOfBoundsException
- ifallele1 < 0 || allele1 >= this.marker(marker).nAlleles()
java.lang.IndexOutOfBoundsException
- ifallele2 < 0 || allele2 >= this.marker(marker).nAlleles()
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