SAMInFormatter

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. final def asInstanceOf[T0]: T0

   Definition Classes

   Any

7. def clone(): AnyRef

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

8. val companion: SAMInFormatter.type

   Attributes

   protected

   Definition Classes

   SAMInFormatter → InFormatter

9. val converter: AlignmentRecordConverter

   A converter from AlignmentRecord to SAMRecord.

   A converter from AlignmentRecord to SAMRecord.

   Definition Classes

   SAMInFormatter → AnySAMInFormatter

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

    Definition Classes

    AnyRef

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. val header: SAMFileHeaderWritable

    A serializable form of the SAM File Header.

    A serializable form of the SAM File Header.

    Definition Classes

    SAMInFormatter → AnySAMInFormatter

14. final def isInstanceOf[T0]: Boolean

    Definition Classes

    Any

15. def makeWriter(os: OutputStream): SAMFileWriter

    Attributes

    protected

    Definition Classes

    SAMInFormatter → AnySAMInFormatter

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

    Definition Classes

    AnyRef

17. final def notify(): Unit

    Definition Classes

    AnyRef

18. final def notifyAll(): Unit

    Definition Classes

    AnyRef

19. val recordGroups: RecordGroupDictionary

    A dictionary describing the read groups these reads are from.

    A dictionary describing the read groups these reads are from.

    Definition Classes

    SAMInFormatter → AnySAMInFormatter

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

    Definition Classes

    AnyRef

21. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

23. final def wait(arg0: Long): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

24. def write(os: OutputStream, iter: Iterator[AlignmentRecord]): Unit

    Writes alignment records to an output stream in SAM format.

    Writes alignment records 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