SequenceDictionary

Value Members

1. final def !=(arg0: Any): Boolean

   

   Definition Classes

   AnyRef → Any

2. final def ##(): Int

   

   Definition Classes

   AnyRef → Any

3. def +(record: SequenceRecord): SequenceDictionary

   

4. def ++(that: SequenceDictionary): SequenceDictionary

   

5. final def ==(arg0: Any): Boolean

   

   Definition Classes

   AnyRef → Any

6. def apply(name: String): Option[SequenceRecord]

   

7. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

8. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

   AnyRef

   Annotations

   @throws( ... )

9. def containsRefName(name: String): Boolean

   

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

    

    Definition Classes

    AnyRef

11. def equals(o: Any): Boolean

    

    Definition Classes

    SequenceDictionary → AnyRef → Any

12. def finalize(): Unit

    

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

    @throws( classOf[java.lang.Throwable] )

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

    

    Definition Classes

    AnyRef → Any

14. def hashCode(): Int

    

    Definition Classes

    SequenceDictionary → AnyRef → Any

15. def isCompatibleWith(that: SequenceDictionary): Boolean

    

16. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

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

    

    Definition Classes

    AnyRef

18. final def notify(): Unit

    

    Definition Classes

    AnyRef

19. final def notifyAll(): Unit

    

    Definition Classes

    AnyRef

20. val records: Vector[SequenceRecord]

    

21. def sorted: SequenceDictionary

    

    Sort the records in a sequence dictionary.

    Sort the records in a sequence dictionary.

    returns

    Returns a new sequence dictionary where the sequence records are sorted. If the sequence records have indices, the records will be sorted by their indices. If not, the sequence records will be sorted lexically by contig name.

    See also

    stripIndices

22. def stripIndices: SequenceDictionary

    

    Strips indices from a Sequence Dictionary.

    Strips indices from a Sequence Dictionary.

    returns

    This returns a new sequence dictionary devoid of indices. This is important for sorting: the default sort in ADAM is based on a lexical ordering, while the default sort in SAM is based on sequence indices. If the indices are not stripped before a file is saved back to SAM/BAM, the SAM/BAM header sequence ordering will not match the sort order of the records in the file.

    See also

    sorted

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

    

    Definition Classes

    AnyRef

24. def toSAMSequenceDictionary: SAMSequenceDictionary

    

    Converts this ADAM style sequence dictionary into a SAM style sequence dictionary.

    Converts this ADAM style sequence dictionary into a SAM style sequence dictionary.

    returns

    Returns a SAM formatted sequence dictionary.

25. def toString(): String

    

    Definition Classes

    SequenceDictionary → AnyRef → Any

26. final def wait(): Unit

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )