ADAM_2.12: Core 1.0.1 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 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

o

org.bdgenomics.adam.ds.read

# SAMInFormatter 

###
Companion class SAMInFormatter

#### object SAMInFormatter extends AnySAMInFormatterCompanion[SAMInFormatter] with Serializable

InFormatter companion for building an InFormatter that streams SAM.

Linear Supertypes
Serializable, Serializable, AnySAMInFormatterCompanion[SAMInFormatter], InFormatterCompanion[Alignment, Alignment, AlignmentDataset, SAMInFormatter], AnyRef, Any
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Ordering

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2. By Inheritance

Inherited

1. SAMInFormatter
2. Serializable
3. Serializable
4. AnySAMInFormatterCompanion
5. InFormatterCompanion
6. AnyRef
7. Any

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Visibility

1. Public
2. All

### 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.  def apply(gDataset: AlignmentDataset): SAMInFormatter

   Makes an AnySAMInFormatter from a GenomicDataset of Alignments.

   Makes an AnySAMInFormatter from a GenomicDataset of Alignments.

   gDataset

     AlignmentDataset with reference build and read group info.

   returns

     Returns an InFormatter that extends AnySAMInFormatter.

   Definition Classes
     AnySAMInFormatterCompanion → InFormatterCompanion
5.  final def asInstanceOf[T0]: T0
   Definition Classes
     Any
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 hashCode(): Int
    Definition Classes
      AnyRef → Any
    Annotations
      @native() @HotSpotIntrinsicCandidate()
11.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
12.  def makeFormatter(header: SAMFileHeader, readGroups: ReadGroupDictionary, converter: AlignmentConverter): SAMInFormatter
    Attributes
      protected
    Definition Classes
      SAMInFormatter → AnySAMInFormatterCompanion
13.  final def ne(arg0: AnyRef): Boolean
    Definition Classes
      AnyRef
14.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
15.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
16.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
17.  def toString(): String
    Definition Classes
      AnyRef → Any
18.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
19.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
20.  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

### Inherited from Serializable

### Inherited from AnySAMInFormatterCompanion[SAMInFormatter]

### Inherited from InFormatterCompanion[Alignment, Alignment, AlignmentDataset, SAMInFormatter]

### Inherited from AnyRef

### Inherited from Any

### Ungrouped