Package | Description |
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htsjdk.variant.variantcontext |
Modifier and Type | Class and Description |
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class |
LazyGenotypesContext
Lazy-loading GenotypesContext.
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Modifier and Type | Field and Description |
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protected GenotypesContext |
VariantContext.genotypes
A mapping from sampleName -> genotype objects for all genotypes associated with this context
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static GenotypesContext |
GenotypesContext.NO_GENOTYPES
static constant value for an empty GenotypesContext.
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static GenotypesContext |
VariantContext.NO_GENOTYPES |
Modifier and Type | Method and Description |
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static GenotypesContext |
GenotypesContext.copy(java.util.Collection<Genotype> toCopy)
Create a GenotypesContext containing the genotypes in iteration order contained
in toCopy
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static GenotypesContext |
GenotypesContext.copy(GenotypesContext toCopy)
Create a freshly allocated GenotypeContext containing the genotypes in toCopy
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static GenotypesContext |
GenotypesContext.create()
Basic creation routine
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static GenotypesContext |
GenotypesContext.create(java.util.ArrayList<Genotype> genotypes)
Create a fully resolved GenotypeContext containing genotypes
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static GenotypesContext |
GenotypesContext.create(java.util.ArrayList<Genotype> genotypes,
java.util.Map<java.lang.String,java.lang.Integer> sampleNameToOffset,
java.util.List<java.lang.String> sampleNamesInOrder)
Create a fully resolved GenotypeContext containing genotypes, sample lookup table,
and sorted sample names
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static GenotypesContext |
GenotypesContext.create(Genotype... genotypes)
Create a fully resolved GenotypeContext containing genotypes
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static GenotypesContext |
GenotypesContext.create(int nGenotypes)
Basic creation routine
|
GenotypesContext |
VariantContext.getGenotypes() |
protected GenotypesContext |
VariantContext.getGenotypes(java.util.Collection<java.lang.String> sampleNames)
Returns a map from sampleName -> Genotype for each sampleName in sampleNames.
|
GenotypesContext |
VariantContext.getGenotypes(java.util.Set<java.lang.String> sampleNames) |
GenotypesContext |
VariantContext.getGenotypes(java.lang.String sampleName)
Returns a map from sampleName -> Genotype for the genotype associated with sampleName.
|
GenotypesContext |
GenotypesContext.immutable() |
GenotypesContext |
GenotypesContext.subsetToSamples(java.util.Set<java.lang.String> samples)
Return a freshly allocated subcontext of this context containing only the samples
listed in samples.
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Modifier and Type | Method and Description |
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static GenotypesContext |
GenotypesContext.copy(GenotypesContext toCopy)
Create a freshly allocated GenotypeContext containing the genotypes in toCopy
|
VariantContextBuilder |
VariantContextBuilder.genotypes(GenotypesContext genotypes)
Tells this builder that the resulting
VariantContext should use this genotype's GenotypeContext . |
VariantContextBuilder |
VariantContextBuilder.genotypesNoValidation(GenotypesContext genotypes) |
Constructor and Description |
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VariantContext(java.lang.String source,
java.lang.String ID,
java.lang.String contig,
long start,
long stop,
java.util.Collection<Allele> alleles,
GenotypesContext genotypes,
double log10PError,
java.util.Set<java.lang.String> filters,
java.util.Map<java.lang.String,java.lang.Object> attributes,
boolean fullyDecoded,
java.util.EnumSet<VariantContext.Validation> validationToPerform)
the actual constructor.
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