Class/Object

org.bdgenomics.adam.models

VariantContext

Related Docs: object VariantContext | package models

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class VariantContext extends Serializable

A representation of all variation data at a single variant.

This class represents an equivalent to a single allele from a VCF line, and is the ADAM equivalent to htsjdk.variant.variantcontext.VariantContext.

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Serializable, Serializable, AnyRef, Any

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Instance Constructors

new VariantContext(position: ReferencePosition, variant: RichVariant, genotypes: Iterable[Genotype])

position
The locus that the variant is at.
variant
The variant allele that is contained in this VariantContext.
genotypes
An iterable collection of Genotypes where this allele was called. Equivalent to the per-sample FORMAT fields in a VCF.

Value Members

final def !=(arg0: Any): Boolean

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final def ##(): Int

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final def ==(arg0: Any): Boolean

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final def asInstanceOf[T0]: T0

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def clone(): AnyRef

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protected[java.lang]
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@throws( ... )
final def eq(arg0: AnyRef): Boolean

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def equals(arg0: Any): Boolean

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def finalize(): Unit

Attributes
protected[java.lang]
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@throws( classOf[java.lang.Throwable] )
val genotypes: Iterable[Genotype]

An iterable collection of Genotypes where this allele was called.
An iterable collection of Genotypes where this allele was called. Equivalent to the per-sample FORMAT fields in a VCF.
final def getClass(): Class[_]

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def hashCode(): Int

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final def isInstanceOf[T0]: Boolean

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final def ne(arg0: AnyRef): Boolean

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final def notify(): Unit

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final def notifyAll(): Unit

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val position: ReferencePosition

The locus that the variant is at.
final def synchronized[T0](arg0: ⇒ T0): T0

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def toString(): String

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val variant: RichVariant

The variant allele that is contained in this VariantContext.
final def wait(): Unit

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@throws( ... )
final def wait(arg0: Long, arg1: Int): Unit

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final def wait(arg0: Long): Unit

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