t

org.bdgenomics.adam.ds.read

AnySAMInFormatterCompanion

trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[Alignment, Alignment, AlignmentDataset, T]

Companion object that builds an InFormatter that writes data where the metadata is contained in a SAMFileHeaderWritable.

T

The type of the underlying InFormatter.

Linear Supertypes
InFormatterCompanion[Alignment, Alignment, AlignmentDataset, T], AnyRef, Any
Known Subclasses
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  1. AnySAMInFormatterCompanion
  2. InFormatterCompanion
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Abstract Value Members

  1. abstract def makeFormatter(header: SAMFileHeader, readGroups: ReadGroupDictionary, converter: AlignmentConverter): T
    Attributes
    protected

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. def apply(gDataset: AlignmentDataset): T

    Makes an AnySAMInFormatter from a GenomicDataset of Alignments.

    Makes an AnySAMInFormatter from a GenomicDataset of Alignments.

    gDataset

    AlignmentDataset with reference build and read group info.

    returns

    Returns an InFormatter that extends AnySAMInFormatter.

    Definition Classes
    AnySAMInFormatterCompanionInFormatterCompanion
  5. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  6. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  7. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  8. def equals(arg0: Any): Boolean
    Definition Classes
    AnyRef → Any
  9. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  10. def hashCode(): Int
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  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() @HotSpotIntrinsicCandidate()
  14. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  15. final def synchronized[T0](arg0: ⇒ T0): T0
    Definition Classes
    AnyRef
  16. def toString(): String
    Definition Classes
    AnyRef → Any
  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( ... ) @native()
  19. 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 InFormatterCompanion[Alignment, Alignment, AlignmentDataset, T]

Inherited from AnyRef

Inherited from Any

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