c

org.bdgenomics.adam.ds.read

ADAMCRAMOutputFormat

class ADAMCRAMOutputFormat[K] extends KeyIgnoringCRAMOutputFormat[K] with Serializable

Wrapper for Hadoop-BAM to work around requirement for no-args constructor.

K

The key type. Keys are not written.

Linear Supertypes
Serializable, Serializable, KeyIgnoringCRAMOutputFormat[K], CRAMOutputFormat[K], FileOutputFormat[K, SAMRecordWritable], OutputFormat[K, SAMRecordWritable], AnyRef, Any
Ordering
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  2. By Inheritance
Inherited
  1. ADAMCRAMOutputFormat
  2. Serializable
  3. Serializable
  4. KeyIgnoringCRAMOutputFormat
  5. CRAMOutputFormat
  6. FileOutputFormat
  7. OutputFormat
  8. AnyRef
  9. Any
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Visibility
  1. Public
  2. All

Instance Constructors

  1. new ADAMCRAMOutputFormat()

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( ... ) @throws( classOf[java.io.IOException] )
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  10. def getDefaultWorkFile(arg0: TaskAttemptContext, arg1: String): Path
    Definition Classes
    FileOutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  11. def getOutputCommitter(arg0: TaskAttemptContext): OutputCommitter
    Definition Classes
    FileOutputFormat → OutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  12. def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable]
    Definition Classes
    ADAMCRAMOutputFormat → KeyIgnoringCRAMOutputFormat → FileOutputFormat → OutputFormat
  13. def getRecordWriter(arg0: TaskAttemptContext, arg1: Path): RecordWriter[K, SAMRecordWritable]
    Definition Classes
    KeyIgnoringCRAMOutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  14. def getSAMHeader(): SAMFileHeader
    Definition Classes
    KeyIgnoringCRAMOutputFormat
  15. def getWriteHeader(): Boolean
    Definition Classes
    KeyIgnoringCRAMOutputFormat
  16. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  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
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  20. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  21. def readSAMHeaderFrom(arg0: InputStream, arg1: Configuration): Unit
    Definition Classes
    KeyIgnoringCRAMOutputFormat
  22. def readSAMHeaderFrom(arg0: Path, arg1: Configuration): Unit
    Definition Classes
    KeyIgnoringCRAMOutputFormat
    Annotations
    @throws( classOf[java.io.IOException] )
  23. def setSAMHeader(arg0: SAMFileHeader): Unit
    Definition Classes
    KeyIgnoringCRAMOutputFormat
  24. def setWriteHeader(arg0: Boolean): Unit
    Definition Classes
    KeyIgnoringCRAMOutputFormat
  25. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  26. def toString(): String
    Definition Classes
    AnyRef → Any
  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( ... ) @native()
  29. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from Serializable

Inherited from Serializable

Inherited from KeyIgnoringCRAMOutputFormat[K]

Inherited from CRAMOutputFormat[K]

Inherited from FileOutputFormat[K, SAMRecordWritable]

Inherited from OutputFormat[K, SAMRecordWritable]

Inherited from AnyRef

Inherited from Any

Ungrouped