org.hammerlab.guacamole.variants

GenotypeOutputArgs

trait GenotypeOutputArgs extends Args4jBase with ParquetArgs

Arguments for writing output genotypes.

Supports writing VCF, JSON, and Parquet formats.

Self Type
GenotypeOutputArgs with Args
Linear Supertypes
ParquetArgs, ParquetRDDArgs, Args4jBase, AnyRef, Any
Known Subclasses
Arguments, Arguments, GermlineCallerArgs
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Inherited
  1. GenotypeOutputArgs
  2. ParquetArgs
  3. ParquetRDDArgs
  4. Args4jBase
  5. AnyRef
  6. Any
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Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. var blockSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  8. def clone(): AnyRef

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  9. var compressionCodec: CompressionCodecName

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  10. var disableDictionaryEncoding: Boolean

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  11. var doPrintUsage: Boolean

    Definition Classes
    Args4jBase

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

    Definition Classes
    AnyRef

  13. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  14. def finalize(): Unit

    Attributes
    protected[java.lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )

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

    Definition Classes
    AnyRef → Any

  16. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  17. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  18. var logLevel: String

    Definition Classes
    ParquetArgs

  19. var maxGenotypes: Int

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

    Definition Classes
    AnyRef

  21. final def notify(): Unit

    Definition Classes
    AnyRef

  22. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  23. var outChunks: Int

  24. lazy val outputPathStr: String

  25. var pageSize: Int

    Definition Classes
    ParquetArgs → ParquetRDDArgs

  26. var printMetrics: Boolean

    Definition Classes
    Args4jBase

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

    Definition Classes
    AnyRef

  28. def toString(): String

    Definition Classes
    AnyRef → Any

  29. def validate(sc: SparkContext): Unit

    Perform validation of command line arguments at startup.

    Perform validation of command line arguments at startup. This allows some late failures (e.g. output file already exists) to be surfaced more quickly.

  30. var variantOutput: String

  31. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

  34. def writeVariants(genotypes: GenotypeRDD): Unit

    Write out an RDD of Genotype instances to a file.

    Write out an RDD of Genotype instances to a file.

    genotypes

    ADAM genotypes (i.e. the variants)

Inherited from ParquetArgs

Inherited from ParquetRDDArgs

Inherited from Args4jBase

Inherited from AnyRef

Inherited from Any

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