org.bdgenomics.adam.rdd.read

# AnySAMInFormatter

###
Related Doc: package read

#### 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
BAMInFormatter, SAMInFormatter
Ordering

1. Alphabetic
2. By Inheritance

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

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

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

   Definition Classes
     AnyRef → Any

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

    Definition Classes
      AnyRef → Any

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

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

    Definition Classes
      AnyRef

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( ... )

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
      AnySAMInFormatter → InFormatter

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

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped