org.bdgenomics.adam.rdd.read

AnySAMInFormatterCompanion

trait AnySAMInFormatterCompanion[T <: AnySAMInFormatter[T]] extends InFormatterCompanion[AlignmentRecord, AlignmentRecordRDD, 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[AlignmentRecord, AlignmentRecordRDD, T], AnyRef, Any
Known Subclasses
BAMInFormatter, SAMInFormatter
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Inherited
  1. AnySAMInFormatterCompanion
  2. InFormatterCompanion
  3. AnyRef
  4. Any
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Abstract Value Members

  1. abstract def makeFormatter(header: SAMFileHeaderWritable, recordGroups: RecordGroupDictionary, converter: AlignmentRecordConverter): T

    Attributes
    protected

Concrete 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. def apply(gRdd: AlignmentRecordRDD): T

    Makes an AnySAMInFormatter from a GenomicRDD of AlignmentRecords.

    Makes an AnySAMInFormatter from a GenomicRDD of AlignmentRecords.

    gRdd

    AlignmentRecordRDD with reference build and record group info.

    returns

    Returns an InFormatter that extends AnySAMInFormatter.

    Definition Classes
    AnySAMInFormatterCompanion → InFormatterCompanion

  7. final def asInstanceOf[T0]: T0

    Definition Classes
    Any

  8. def clone(): AnyRef

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

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

    Definition Classes
    AnyRef

  10. def equals(arg0: Any): Boolean

    Definition Classes
    AnyRef → Any

  11. def finalize(): Unit

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

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

    Definition Classes
    AnyRef → Any

  13. def hashCode(): Int

    Definition Classes
    AnyRef → Any

  14. final def isInstanceOf[T0]: Boolean

    Definition Classes
    Any

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

    Definition Classes
    AnyRef

  16. final def notify(): Unit

    Definition Classes
    AnyRef

  17. final def notifyAll(): Unit

    Definition Classes
    AnyRef

  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 InFormatterCompanion[AlignmentRecord, AlignmentRecordRDD, T]

Inherited from AnyRef

Inherited from Any

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