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

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org.bdgenomics.adam.rdd.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[AlignmentRecord, AlignmentRecord, AlignmentRecordDataset, 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: AlignmentRecordDataset): SAMInFormatter

   Makes an AnySAMInFormatter from a GenomicDataset of AlignmentRecords.

   Makes an AnySAMInFormatter from a GenomicDataset of AlignmentRecords.

   gDataset

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

### Inherited from Serializable

### Inherited from AnySAMInFormatterCompanion[SAMInFormatter]

### Inherited from InFormatterCompanion[AlignmentRecord, AlignmentRecord, AlignmentRecordDataset, SAMInFormatter]

### Inherited from AnyRef

### Inherited from Any

### Ungrouped