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
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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
  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
    AnySAMOutFormatterOutFormatter
  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
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

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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