org.bdgenomics.adam.rdd.read

# SAMInFormatter

###
Related Docs: object SAMInFormatter | package read

#### case class SAMInFormatter extends AnySAMInFormatter[SAMInFormatter] with Product with Serializable

Linear Supertypes
Product, Equals, AnySAMInFormatter[SAMInFormatter], InFormatter[Alignment, Alignment, AlignmentDataset, SAMInFormatter], Serializable, Serializable, AnyRef, Any
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Inherited

1. SAMInFormatter
2. Product
3. Equals
4. AnySAMInFormatter
5. InFormatter
6. Serializable
7. Serializable
8. AnyRef
9. Any

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Visibility

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### Instance Constructors

1. #### new SAMInFormatter()

### 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. #### val companion: SAMInFormatter.type

   Attributes
     protected
   Definition Classes
     SAMInFormatter → InFormatter

7. #### val converter: AlignmentConverter

   A converter from Alignment to SAMRecord.

   A converter from Alignment to SAMRecord.

   Definition Classes
     SAMInFormatter → AnySAMInFormatter

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

   Definition Classes
     AnyRef

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. #### val header: SAMFileHeader

    A serializable form of the SAM File Header.

    A serializable form of the SAM File Header.

    Definition Classes
      SAMInFormatter → AnySAMInFormatter

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

    Definition Classes
      Any

13. #### def makeWriter(os: OutputStream): SAMFileWriter

    Attributes
      protected
    Definition Classes
      SAMInFormatter → AnySAMInFormatter

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

17. #### val readGroups: ReadGroupDictionary

    A dictionary describing the read groups these reads are from.

    A dictionary describing the read groups these reads are from.

    Definition Classes
      SAMInFormatter → AnySAMInFormatter

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

22. #### 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 Product

### Inherited from Equals

### Inherited from AnySAMInFormatter[SAMInFormatter]

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

### Inherited from Serializable

### Inherited from AnyRef

### Inherited from Any

### Ungrouped