ADAM_2.12: Core 0.29.0 API < Back
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# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package rdd
  Definition Classes
    adam
-  package read
  Definition Classes
    rdd
- ADAMBAMOutputFormat
- ADAMBAMOutputFormatHeaderLess
- ADAMCRAMOutputFormat
- ADAMCRAMOutputFormatHeaderLess
- ADAMSAMOutputFormat
- ADAMSAMOutputFormatHeaderLess
- AlignmentRecordDataset
- AnySAMInFormatter
- AnySAMInFormatterCompanion
- AnySAMOutFormatter
- BAMInFormatter
- DatasetBoundAlignmentRecordDataset
- DatasetBoundReadDataset
- FASTQInFormatter
- IncorrectMDTagException
- InstrumentedADAMBAMOutputFormat
- InstrumentedADAMBAMOutputFormatHeaderLess
- InstrumentedADAMCRAMOutputFormat
- InstrumentedADAMCRAMOutputFormatHeaderLess
- InstrumentedADAMSAMOutputFormat
- InstrumentedADAMSAMOutputFormatHeaderLess
- ParquetUnboundAlignmentRecordDataset
- ParquetUnboundReadDataset
- QualityScoreBin
- RDDBoundAlignmentRecordDataset
- RDDBoundReadDataset
- ReadDataset
- ReferencePositionPairSerializer
- SAMInFormatter
- SingleReadBucketSerializer

c

org.bdgenomics.adam.rdd.read

# ADAMBAMOutputFormat 

###

#### 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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Ordering

1. Alphabetic
2. By Inheritance

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
     @native() @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
    Annotations
      @native()
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
    Annotations
      @native()
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
    Annotations
      @native()
21.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native()
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
      @native() @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