org.bdgenomics.adam.rdd.read

# AnySAMOutFormatter

###
Related Doc: package read

#### 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
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Inherited

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

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Visibility

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### 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[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( ... )

6. #### final def eq(arg0: AnyRef): Boolean

   Definition Classes
     AnyRef

7. #### def finalize(): Unit

   Attributes
     protected[java.lang]
   Definition Classes
     AnyRef
   Annotations
     @throws( classOf[java.lang.Throwable] )

8. #### final def getClass(): Class[_]

   Definition Classes
     AnyRef → Any

9. #### final def isInstanceOf[T0]: Boolean

   Definition Classes
     Any

10. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

11. #### final def notify(): Unit

    Definition Classes
      AnyRef

12. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

13. #### 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

14. #### val stringency: ValidationStringency

15. #### final def synchronized[T0](arg0: ⇒ T0): T0

    Definition Classes
      AnyRef

16. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

17. #### final def wait(arg0: Long, arg1: Int): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

18. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from Product

### Inherited from Equals

### Inherited from OutFormatter[Alignment]

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped