Package | Description |
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htsjdk.variant.variantcontext |
Modifier and Type | Method and Description |
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VariantContextBuilder |
VariantContextBuilder.alleles(java.util.Collection<Allele> alleles)
Tells this builder to use this collection of alleles for the resulting VariantContext
|
VariantContextBuilder |
VariantContextBuilder.alleles(java.util.List<java.lang.String> alleleStrings) |
VariantContextBuilder |
VariantContextBuilder.alleles(java.lang.String... alleleStrings) |
VariantContextBuilder |
VariantContextBuilder.attribute(java.lang.String key,
java.lang.Object value)
Puts the key -> value mapping into this builder's attributes
|
VariantContextBuilder |
VariantContextBuilder.attributes(java.util.Map<java.lang.String,java.lang.Object> attributes)
Tells this builder to use this map of attributes alleles for the resulting
VariantContext
Attributes can be null -> meaning there are no attributes. |
VariantContextBuilder |
VariantContextBuilder.chr(java.lang.String contig)
Tells us that the resulting VariantContext should have the specified contig chr
|
VariantContextBuilder |
VariantContextBuilder.computeEndFromAlleles(java.util.List<Allele> alleles,
int start) |
VariantContextBuilder |
VariantContextBuilder.computeEndFromAlleles(java.util.List<Allele> alleles,
int start,
int endForSymbolicAlleles)
Compute the end position for this VariantContext from the alleles themselves
assigns this builder the stop position computed.
|
VariantContextBuilder |
VariantContextBuilder.copy() |
VariantContextBuilder |
VariantContextBuilder.filter(java.lang.String filter) |
VariantContextBuilder |
VariantContextBuilder.filters(java.util.Set<java.lang.String> filters)
This builder's filters are set to this value
filters can be
null -> meaning there are no filters |
VariantContextBuilder |
VariantContextBuilder.filters(java.lang.String... filters)
|
VariantContextBuilder |
VariantContextBuilder.fullyDecoded(boolean isFullyDecoded)
Sets this builder's fully decoded state to true.
|
VariantContextBuilder |
VariantContextBuilder.genotypes(java.util.Collection<Genotype> genotypes)
Tells this builder that the resulting
VariantContext should use a GenotypeContext containing genotypes
Note that genotypes can be null , meaning there are no genotypes |
VariantContextBuilder |
VariantContextBuilder.genotypes(Genotype... genotypes)
Tells this builder that the resulting
VariantContext should use a GenotypeContext containing genotypes |
VariantContextBuilder |
VariantContextBuilder.genotypes(GenotypesContext genotypes)
Tells this builder that the resulting
VariantContext should use this genotype's GenotypeContext . |
VariantContextBuilder |
VariantContextBuilder.genotypesNoValidation(GenotypesContext genotypes) |
VariantContextBuilder |
VariantContextBuilder.id(java.lang.String ID)
Tells us that the resulting VariantContext should have ID
|
VariantContextBuilder |
VariantContextBuilder.loc(java.lang.String contig,
long start,
long stop)
Tells us that the resulting VariantContext should have the specified location
|
VariantContextBuilder |
VariantContextBuilder.log10PError(double log10PError)
Tells us that the resulting VariantContext should have log10PError
|
VariantContextBuilder |
VariantContextBuilder.noGenotypes()
Tells this builder that the resulting VariantContext should not contain any GenotypeContext
|
VariantContextBuilder |
VariantContextBuilder.noID()
Tells us that the resulting VariantContext should not have an ID
|
VariantContextBuilder |
VariantContextBuilder.passFilters()
Tells this builder that the resulting VariantContext should have PASS filters
|
VariantContextBuilder |
VariantContextBuilder.rmAttribute(java.lang.String key)
Removes key if present in the attributes
|
VariantContextBuilder |
VariantContextBuilder.rmAttributes(java.util.List<java.lang.String> keys)
Removes list of keys if present in the attributes
|
VariantContextBuilder |
VariantContextBuilder.source(java.lang.String source)
Tells us that the resulting VariantContext should have source field set to source
|
VariantContextBuilder |
VariantContextBuilder.start(long start)
Tells us that the resulting VariantContext should have the specified contig start
|
VariantContextBuilder |
VariantContextBuilder.stop(long stop)
Tells us that the resulting VariantContext should have the specified contig stop
|
VariantContextBuilder |
VariantContextBuilder.unfiltered()
Tells this builder that the resulting VariantContext be unfiltered
|
Modifier and Type | Method and Description |
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static void |
VariantContextUtils.calculateChromosomeCounts(VariantContextBuilder builder,
boolean removeStaleValues)
Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper
chromosome-based VCF tags based on the current VC produced by builder.make()
|
static void |
VariantContextUtils.calculateChromosomeCounts(VariantContextBuilder builder,
boolean removeStaleValues,
java.util.Set<java.lang.String> founderIds)
Update the attributes of the attributes map in the VariantContextBuilder to reflect the proper
chromosome-based VCF tags based on the current VC produced by builder.make()
|
Constructor and Description |
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VariantContextBuilder(VariantContextBuilder parent) |