ADAM_2.12: Core 1.0.1 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

# AnySAMOutFormatter 

###

#### case class AnySAMOutFormatter(stringency: ValidationStringency) extends OutFormatter[Alignment] with Product with Serializable

An OutFormatter that automatically infers whether the piped input is SAM or BAM. Autodetecting streamed CRAM is not currently supported.

Linear Supertypes
Product, Equals, OutFormatter[Alignment], Serializable, Serializable, AnyRef, Any
 
Ordering

1. Alphabetic
2. By Inheritance

Inherited

1. AnySAMOutFormatter
2. Product
3. Equals
4. OutFormatter
5. Serializable
6. Serializable
7. AnyRef
8. Any

1. Hide All
2. Show All

Visibility

1. Public
2. All

### Instance Constructors

1.  new AnySAMOutFormatter()
2.  new AnySAMOutFormatter(stringency: ValidationStringency)

### 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.  final def eq(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
7.  final def getClass(): Class[_]
   Definition Classes
     AnyRef → Any
   Annotations
     @native() @HotSpotIntrinsicCandidate()
8.  final def isInstanceOf[T0]: Boolean
   Definition Classes
     Any
9.  final def ne(arg0: AnyRef): Boolean
   Definition Classes
     AnyRef
10.  final def notify(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
11.  final def notifyAll(): Unit
    Definition Classes
      AnyRef
    Annotations
      @native() @HotSpotIntrinsicCandidate()
12.  def read(is: InputStream): Iterator[Alignment]

    Reads alignments from an input stream.

    Reads alignments from an input stream. Autodetects SAM/BAM format.

    is

      An InputStream connected to a process we are piping from.

    returns

      Returns an iterator of Alignments read from the stream.

    Definition Classes
      AnySAMOutFormatter → OutFormatter
13.  val stringency: ValidationStringency
14.  final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
      AnyRef
15.  final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... )
16.  final def wait(arg0: Long): Unit
    Definition Classes
      AnyRef
    Annotations
      @throws( ... ) @native()
17.  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 Product

### Inherited from Equals

### Inherited from OutFormatter[Alignment]

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped