org.bdgenomics.adam.rdd.variation

ADAMVCFOutputFormat

class ADAMVCFOutputFormat[K] extends KeyIgnoringVCFOutputFormat[K] with Serializable

Wrapper for Hadoop-BAM to work around requirement for no-args constructor. Depends on ADAMVCFOutputFormat object to maintain global state (such as samples)

K

Linear Supertypes
Serializable, Serializable, KeyIgnoringVCFOutputFormat[K], VCFOutputFormat[K], FileOutputFormat[K, VariantContextWritable], OutputFormat[K, VariantContextWritable], AnyRef, Any
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Inherited
  1. ADAMVCFOutputFormat
  2. Serializable
  3. Serializable
  4. KeyIgnoringVCFOutputFormat
  5. VCFOutputFormat
  6. FileOutputFormat
  7. OutputFormat
  8. AnyRef
  9. Any
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Visibility
  1. Public
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Instance Constructors

  1. new ADAMVCFOutputFormat()

Value Members

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

    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

    Definition Classes
    AnyRef → Any

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

    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  5. def checkOutputSpecs(arg0: JobContext): Unit

    Definition Classes
    FileOutputFormat → OutputFormat
    Annotations
    @throws( classOf[java.io.IOException] ) @throws( ... )

  6. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  8. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  9. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  11. def getDefaultWorkFile(arg0: TaskAttemptContext, arg1: String): Path

    Definition Classes
    FileOutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )

  12. def getHeader(): VCFHeader

    Definition Classes
    KeyIgnoringVCFOutputFormat

  13. def getOutputCommitter(arg0: TaskAttemptContext): OutputCommitter

    Definition Classes
    FileOutputFormat → OutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )

  14. def getRecordWriter(arg0: TaskAttemptContext, arg1: Path): RecordWriter[K, VariantContextWritable]

    Definition Classes
    KeyIgnoringVCFOutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )

  15. def getRecordWriter(arg0: TaskAttemptContext): RecordWriter[K, VariantContextWritable]

    Definition Classes
    KeyIgnoringVCFOutputFormat → FileOutputFormat → OutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )

  16. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  17. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  19. final def notify(): Unit

    Definition Classes
    AnyRef

  20. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  21. def readHeaderFrom(arg0: SeekableStream): Unit

    Definition Classes
    KeyIgnoringVCFOutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )

  22. def readHeaderFrom(arg0: Path, arg1: FileSystem): Unit

    Definition Classes
    KeyIgnoringVCFOutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )

  23. def setHeader(arg0: VCFHeader): Unit

    Definition Classes
    KeyIgnoringVCFOutputFormat

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

    Definition Classes
    AnyRef

  25. def toString(): String

    Definition Classes
    AnyRef → Any

  26. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Serializable

Inherited from Serializable

Inherited from KeyIgnoringVCFOutputFormat[K]

Inherited from VCFOutputFormat[K]

Inherited from FileOutputFormat[K, VariantContextWritable]

Inherited from OutputFormat[K, VariantContextWritable]

Inherited from AnyRef

Inherited from Any

Ungrouped