org.bdgenomics.adam.rdd.variation

ADAMVCFOutputFormat

class ADAMVCFOutputFormat[K] extends KeyIgnoringVCFOutputFormat[K]

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
KeyIgnoringVCFOutputFormat[K], VCFOutputFormat[K], FileOutputFormat[K, VariantContextWritable], OutputFormat[K, VariantContextWritable], AnyRef, Any
Ordering
  1. Alphabetic
  2. By inheritance
Inherited
  1. ADAMVCFOutputFormat
  2. KeyIgnoringVCFOutputFormat
  3. VCFOutputFormat
  4. FileOutputFormat
  5. OutputFormat
  6. AnyRef
  7. Any
  1. Hide All
  2. Show all
Learn more about member selection
Visibility
  1. Public
  2. All

Instance Constructors

  1. new ADAMVCFOutputFormat()

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. def checkOutputSpecs(arg0: JobContext): Unit

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

  8. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

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

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

  14. def getHeader(): VCFHeader

    Definition Classes
    KeyIgnoringVCFOutputFormat

  15. def getOutputCommitter(arg0: TaskAttemptContext): OutputCommitter

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

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

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

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

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

  18. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  19. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

  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. def readHeaderFrom(arg0: SeekableStream): Unit

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

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

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

  25. def setHeader(arg0: VCFHeader): Unit

    Definition Classes
    KeyIgnoringVCFOutputFormat

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

    Definition Classes
    AnyRef

  27. def toString(): String

    Definition Classes
    AnyRef → Any

  28. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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