org.bdgenomics.adam.rdd.read

# ADAMBAMOutputFormat

###
Related Doc: package read

#### class ADAMBAMOutputFormat[K] extends KeyIgnoringBAMOutputFormat[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, KeyIgnoringBAMOutputFormat[K], BAMOutputFormat[K], FileOutputFormat[K, SAMRecordWritable], OutputFormat[K, SAMRecordWritable], AnyRef, Any
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Inherited

1. ADAMBAMOutputFormat
2. Serializable
3. Serializable
4. KeyIgnoringBAMOutputFormat
5. BAMOutputFormat
6. FileOutputFormat
7. OutputFormat
8. AnyRef
9. Any

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Visibility

1. Public
2. All

### Instance Constructors

1. #### new ADAMBAMOutputFormat()

### 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 getOutputCommitter(arg0: TaskAttemptContext): OutputCommitter

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

13. #### def getRecordWriter(context: TaskAttemptContext): RecordWriter[K, SAMRecordWritable]

    Definition Classes
      ADAMBAMOutputFormat → KeyIgnoringBAMOutputFormat → FileOutputFormat → OutputFormat

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

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

15. #### def getSAMHeader(): SAMFileHeader

    Definition Classes
      KeyIgnoringBAMOutputFormat

16. #### def getWriteHeader(): Boolean

    Definition Classes
      KeyIgnoringBAMOutputFormat

17. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

18. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

19. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

20. #### final def notify(): Unit

    Definition Classes
      AnyRef

21. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

22. #### def readSAMHeaderFrom(arg0: InputStream, arg1: Configuration): Unit

    Definition Classes
      KeyIgnoringBAMOutputFormat

23. #### def readSAMHeaderFrom(arg0: Path, arg1: Configuration): Unit

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

24. #### def setSAMHeader(arg0: SAMFileHeader): Unit

    Definition Classes
      KeyIgnoringBAMOutputFormat

25. #### def setWriteHeader(arg0: Boolean): Unit

    Definition Classes
      KeyIgnoringBAMOutputFormat

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 Serializable

### Inherited from KeyIgnoringBAMOutputFormat[K]

### Inherited from BAMOutputFormat[K]

### Inherited from FileOutputFormat[K, SAMRecordWritable]

### Inherited from OutputFormat[K, SAMRecordWritable]

### Inherited from AnyRef

### Inherited from Any

### Ungrouped