ADAM_2.12: Core 0.35.0 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 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

# SAMInFormatter 

###
Companion object SAMInFormatter

#### case class SAMInFormatter extends AnySAMInFormatter[SAMInFormatter] with Product with Serializable

Linear Supertypes
Product, Equals, AnySAMInFormatter[SAMInFormatter], InFormatter[Alignment, Alignment, AlignmentDataset, SAMInFormatter], Serializable, Serializable, AnyRef, Any
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Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. SAMInFormatter
2. Product
3. Equals
4. AnySAMInFormatter
5. InFormatter
6. Serializable
7. Serializable
8. AnyRef
9. Any

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Visibility

1. Public
2. All

### Instance Constructors

1.  new SAMInFormatter()

### 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 clone(): AnyRef
   Attributes
     protected[lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... ) @native() @HotSpotIntrinsicCandidate()
6.  val companion: SAMInFormatter.type
   Attributes
     protected
   Definition Classes
     SAMInFormatter → InFormatter
7.  val converter: AlignmentConverter

   A converter from Alignment to SAMRecord.

   A converter from Alignment to SAMRecord.

   Definition Classes
     SAMInFormatter → AnySAMInFormatter
8.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
9.  final def getClass(): Class[_]
   Definition Classes
     AnyRef → Any
   Annotations
     @native() @HotSpotIntrinsicCandidate()
10.  val header: SAMFileHeader

    A serializable form of the SAM File Header.

    A serializable form of the SAM File Header.

    Definition Classes
      SAMInFormatter → AnySAMInFormatter
11.  final def isInstanceOf[T0]: Boolean
    Definition Classes
      Any
12.  def makeWriter(os: OutputStream): SAMFileWriter
    Attributes
      protected
    Definition Classes
      SAMInFormatter → AnySAMInFormatter
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.  val readGroups: ReadGroupDictionary

    A dictionary describing the read groups these reads are from.

    A dictionary describing the read groups these reads are from.

    Definition Classes
      SAMInFormatter → AnySAMInFormatter
17.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
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( ... )
21.  def write(os: OutputStream, iter: Iterator[Alignment]): Unit

    Writes alignments to an output stream in SAM format.

    Writes alignments to an output stream in SAM format.

    os

      An OutputStream connected to a process we are piping to.

    iter

      An iterator of records to write.

    Definition Classes
      AnySAMInFormatter → InFormatter

### 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 Product

### Inherited from Equals

### Inherited from AnySAMInFormatter[SAMInFormatter]

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

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped