ADAM_2.12: Core 1.0 API < Back
 

# Packages

-  package root
  Definition Classes
    root
-  package org
  Definition Classes
    root
-  package bdgenomics
  Definition Classes
    org
-  package adam
  Definition Classes
    bdgenomics
-  package ds
  Definition Classes
    adam
-  package read
  Definition Classes
    ds
- ADAMBAMOutputFormat
- ADAMBAMOutputFormatHeaderLess
- ADAMCRAMOutputFormat
- ADAMCRAMOutputFormatHeaderLess
- ADAMSAMOutputFormat
- ADAMSAMOutputFormatHeaderLess
- AlignmentDataset
- AnySAMInFormatter
- AnySAMInFormatterCompanion
- AnySAMOutFormatter
- BAMInFormatter
- DatasetBoundAlignmentDataset
- DatasetBoundReadDataset
- FASTQInFormatter
- IncorrectMDTagException
- ParquetUnboundAlignmentDataset
- ParquetUnboundReadDataset
- QualityScoreBin
- RDDBoundAlignmentDataset
- RDDBoundReadDataset
- ReadDataset
- ReferencePositionPairSerializer
- SAMInFormatter
- SingleReadBucketSerializer

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

1. Alphabetic
2. By Inheritance

Inherited

1. ADAMCRAMOutputFormat
2. Serializable
3. Serializable
4. KeyIgnoringCRAMOutputFormat
5. CRAMOutputFormat
6. FileOutputFormat
7. OutputFormat
8. AnyRef
9. Any

1. Hide All
2. Show All

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()
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[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
      ADAMCRAMOutputFormat → KeyIgnoringCRAMOutputFormat → FileOutputFormat → OutputFormat
14.  def getRecordWriter(arg0: TaskAttemptContext, arg1: Path): RecordWriter[K, SAMRecordWritable]
    Definition Classes
      KeyIgnoringCRAMOutputFormat
    Annotations
      @throws( classOf[java.io.IOException] )
15.  def getSAMHeader(): SAMFileHeader
    Definition Classes
      KeyIgnoringCRAMOutputFormat
16.  def getWriteHeader(): Boolean
    Definition Classes
      KeyIgnoringCRAMOutputFormat
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
      KeyIgnoringCRAMOutputFormat
23.  def readSAMHeaderFrom(arg0: Path, arg1: Configuration): Unit
    Definition Classes
      KeyIgnoringCRAMOutputFormat
    Annotations
      @throws( classOf[java.io.IOException] )
24.  def setSAMHeader(arg0: SAMFileHeader): Unit
    Definition Classes
      KeyIgnoringCRAMOutputFormat
25.  def setWriteHeader(arg0: Boolean): Unit
    Definition Classes
      KeyIgnoringCRAMOutputFormat
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( ... ) @native()

### 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