org.bdgenomics.adam.converters

VariantContextConverter

class VariantContextConverter extends Serializable with Logging

This class converts VCF data to and from ADAM. This translation occurs at the abstraction level of the htsjdk VariantContext which represents VCF data, and at the ADAMVariantContext level, which aggregates ADAM variant/genotype/annotation data together.

If a genotype annotation has a corresponding set of fields in the VCF standard, a conversion to/from the htsjdk VariantContext should be implemented in this class.

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Instance Constructors

  1. new VariantContextConverter(headerLines: Seq[VCFHeaderLine], stringency: ValidationStringency, setNestedAnnotationInGenotype: Boolean)

Value Members

  1. final def !=(arg0: AnyRef): Boolean

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    AnyRef

  2. final def !=(arg0: Any): Boolean

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  3. final def ##(): Int

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  4. final def ==(arg0: AnyRef): Boolean

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  5. final def ==(arg0: Any): Boolean

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  6. final def asInstanceOf[T0]: T0

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  7. def clone(): AnyRef

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    protected[java.lang]
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    @throws( ... )

  8. def convert(vc: VariantContext): Option[VariantContext]

    Convert an ADAM variant context into a GATK variant context.

    Convert an ADAM variant context into a GATK variant context.

    vc

    ADAM variant context to convert.

    returns

    The specified ADAM variant context converted into a GATK variant context.

  9. def convert(vc: VariantContext): Seq[VariantContext]

    Converts a GATK variant context into one or more ADAM variant context(s).

    Converts a GATK variant context into one or more ADAM variant context(s).

    vc

    GATK variant context to convert.

    returns

    The specified GATK variant context converted into one or more ADAM variant context(s)

  10. final def eq(arg0: AnyRef): Boolean

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  11. def equals(arg0: Any): Boolean

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  12. def finalize(): Unit

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  13. final def getClass(): Class[_]

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  14. def hashCode(): Int

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  15. final def isInstanceOf[T0]: Boolean

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  16. def isTraceEnabled(): Boolean

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  17. def log: Logger

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  18. def logDebug(msg: ⇒ String, throwable: Throwable): Unit

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  19. def logDebug(msg: ⇒ String): Unit

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  20. def logError(msg: ⇒ String, throwable: Throwable): Unit

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  21. def logError(msg: ⇒ String): Unit

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  22. def logInfo(msg: ⇒ String, throwable: Throwable): Unit

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  23. def logInfo(msg: ⇒ String): Unit

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  24. def logName: String

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  25. def logTrace(msg: ⇒ String, throwable: Throwable): Unit

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  26. def logTrace(msg: ⇒ String): Unit

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  27. def logWarning(msg: ⇒ String, throwable: Throwable): Unit

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  28. def logWarning(msg: ⇒ String): Unit

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  29. final def ne(arg0: AnyRef): Boolean

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  30. final def notify(): Unit

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  31. final def notifyAll(): Unit

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  32. final def synchronized[T0](arg0: ⇒ T0): T0

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  33. def toString(): String

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  34. final def wait(): Unit

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

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  36. final def wait(arg0: Long): Unit

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