org.bdgenomics.adam.rdd.read

AnySAMOutFormatter

class AnySAMOutFormatter extends OutFormatter[AlignmentRecord]

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

Linear Supertypes
OutFormatter[AlignmentRecord], Serializable, Serializable, AnyRef, Any
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Inherited
  1. AnySAMOutFormatter
  2. OutFormatter
  3. Serializable
  4. Serializable
  5. AnyRef
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Instance Constructors

  1. new AnySAMOutFormatter()

Value Members

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

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  3. final def ##(): Int

    Definition Classes
    AnyRef → Any

  4. final def ==(arg0: AnyRef): Boolean

    Definition Classes
    AnyRef

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

    Definition Classes
    Any

  6. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  7. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  9. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  10. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  12. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  13. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  15. final def notify(): Unit

    Definition Classes
    AnyRef

  16. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  17. def read(is: InputStream): Iterator[AlignmentRecord]

    Reads alignment records from an input stream.

    Reads alignment records from an input stream. Autodetects SAM/BAM format.

    is

    An InputStream connected to a process we are piping from.

    returns

    Returns an iterator of AlignmentRecords read from the stream.

    Definition Classes
    AnySAMOutFormatter → OutFormatter

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

    Definition Classes
    AnyRef

  19. def toString(): String

    Definition Classes
    AnyRef → Any

  20. final def wait(): Unit

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

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

    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Inherited from OutFormatter[AlignmentRecord]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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