object VariantContextConverter extends Serializable
Object for converting between htsjdk and ADAM VariantContexts.
Handles Variant, Genotype, Allele, and various genotype annotation conversions. Does not handle Variant annotations. Genotype annotations are annotations in the VCF GT field while Variant annotations are annotations contained in the VCF INFO field.
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- def apply(headerLines: Seq[VCFHeaderLine], stringency: ValidationStringency, conf: Configuration): VariantContextConverter
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- def cleanAndMixInSupportedLines(headerLines: Seq[VCFHeaderLine], stringency: ValidationStringency, log: Logger): Seq[VCFHeaderLine]
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def
headerLines(header: VCFHeader): Seq[VCFHeaderLine]
Return the header lines in the specified VCF file header.
Return the header lines in the specified VCF file header.
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VCF file header
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the header lines in the specified VCF file header
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ne(arg0: AnyRef): Boolean
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val
nestAnnotationInGenotypesProperty: String
If set to true, this property will ensure that the variant.annotation field in the Genotype record is populated after conversion from an htsjdk VariantContext.
If set to true, this property will ensure that the variant.annotation field in the Genotype record is populated after conversion from an htsjdk VariantContext. By default, this property is false.
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def
references(header: VCFHeader): SequenceDictionary
Return the references in the specified VCF file header.
Return the references in the specified VCF file header.
- header
VCF file header
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the references in the specified VCF file header
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def
samples(header: VCFHeader): Seq[Sample]
Return the samples in the specified VCF file header.
Return the samples in the specified VCF file header.
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VCF file header
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the samples in the specified VCF file header
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def
setNestAnnotationInGenotypesProperty(conf: Configuration, populateNestedAnn: Boolean): Unit
Sets the value of the nest annotation in genotypes property.
Sets the value of the nest annotation in genotypes property.
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Hadoop configuration to set the property in.
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If true, the nested field is populated.
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