t

org.bdgenomics.adam.ds.read

AnySAMInFormatter

trait AnySAMInFormatter[T <: AnySAMInFormatter[T]] extends InFormatter[Alignment, Alignment, AlignmentDataset, T]

A trait that writes reads using an Htsjdk SAMFileWriter.

T

The recursive type of the class that implements this trait.

Linear Supertypes
InFormatter[Alignment, Alignment, AlignmentDataset, T], Serializable, Serializable, AnyRef, Any
Known Subclasses
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Inherited
  1. AnySAMInFormatter
  2. InFormatter
  3. Serializable
  4. Serializable
  5. AnyRef
  6. Any
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Visibility
  1. Public
  2. All

Abstract Value Members

  1. abstract val companion: InFormatterCompanion[Alignment, Alignment, AlignmentDataset, T]
    Attributes
    protected
    Definition Classes
    InFormatter
  2. abstract val converter: AlignmentConverter

    A converter from Alignment to SAMRecord.

  3. abstract val header: SAMFileHeader

    A serializable form of the SAM File Header.

  4. abstract def makeWriter(os: OutputStream): SAMFileWriter
    Attributes
    protected
  5. abstract val readGroups: ReadGroupDictionary

    A dictionary describing the read groups these reads are from.

Concrete 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()
  6. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  7. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  8. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] )
  9. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  10. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native()
  11. final def isInstanceOf[T0]: Boolean
    Definition Classes
    Any
  12. final def ne(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  13. final def notify(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  14. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native()
  15. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  16. def toString(): String
    Definition Classes
    AnyRef → Any
  17. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  18. final def wait(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  19. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  20. def write(os: OutputStream, iter: Iterator[Alignment]): Unit

    Writes alignments to an output stream in SAM format.

    Writes alignments to an output stream in SAM format.

    os

    An OutputStream connected to a process we are piping to.

    iter

    An iterator of records to write.

    Definition Classes
    AnySAMInFormatterInFormatter

Inherited from InFormatter[Alignment, Alignment, AlignmentDataset, T]

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

Ungrouped