org.bdgenomics.adam.rdd.read

# AnySAMInFormatterCompanion

###
Related Doc: package read

#### 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
BAMInFormatter, SAMInFormatter
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Inherited

1. AnySAMInFormatterCompanion
2. InFormatterCompanion
3. AnyRef
4. Any

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Visibility

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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
     AnySAMInFormatterCompanion → InFormatterCompanion

5. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

6. #### def clone(): AnyRef

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

7. #### final def eq(arg0: AnyRef): Boolean

   Definition Classes
     AnyRef

8. #### def equals(arg0: Any): Boolean

   Definition Classes
     AnyRef → Any

9. #### def finalize(): Unit

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

10. #### final def getClass(): Class[_]

    Definition Classes
      AnyRef → Any

11. #### def hashCode(): Int

    Definition Classes
      AnyRef → Any

12. #### final def isInstanceOf[T0]: Boolean

    Definition Classes
      Any

13. #### final def ne(arg0: AnyRef): Boolean

    Definition Classes
      AnyRef

14. #### final def notify(): Unit

    Definition Classes
      AnyRef

15. #### final def notifyAll(): Unit

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

17. #### def toString(): String

    Definition Classes
      AnyRef → Any

18. #### final def wait(): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

20. #### final def wait(arg0: Long): Unit

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

### Inherited from InFormatterCompanion[Alignment, Alignment, AlignmentDataset, T]

### Inherited from AnyRef

### Inherited from Any

### Ungrouped