Class

org.bdgenomics.adam.rdd.read

AnySAMOutFormatter

Related Doc: package read

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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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Instance Constructors

  1. new AnySAMOutFormatter()

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  2. new AnySAMOutFormatter(stringency: ValidationStringency)

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Value Members

  1. final def !=(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  2. final def ##(): Int

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    Definition Classes
    AnyRef → Any

  3. final def ==(arg0: Any): Boolean

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    Definition Classes
    AnyRef → Any

  4. final def asInstanceOf[T0]: T0

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    Definition Classes
    Any

  5. def clone(): AnyRef

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

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

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    Definition Classes
    AnyRef

  7. def finalize(): Unit

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

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

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    Definition Classes
    AnyRef → Any

  9. final def isInstanceOf[T0]: Boolean

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    Definition Classes
    Any

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

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    Definition Classes
    AnyRef

  11. final def notify(): Unit

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    Definition Classes
    AnyRef

  12. final def notifyAll(): Unit

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    Definition Classes
    AnyRef

  13. def read(is: InputStream): Iterator[Alignment]

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    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

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

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    Definition Classes
    AnyRef

  16. final def wait(): Unit

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

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    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from Product

Inherited from Equals

Inherited from OutFormatter[Alignment]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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