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

   

   Adds a sequence record to this dictionary.

   Adds a sequence record to this dictionary.

   record

   The sequence record to add.

   returns

   A new sequence dictionary with the new record added.

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

   

   Merges two sequence dictionaries.

   Merges two sequence dictionaries.

   Filters any sequence records that exist in both dictionaries.

   that

   The sequence dictionary to add.

   returns

   A new sequence dictionary that contains a record per contig in each input dictionary.

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

   

   Definition Classes

   AnyRef → Any

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

   
   name

   The name of the contig to extract.

   returns

   If available, the sequence record for this contig.

7. final def asInstanceOf[T0]: T0

   

   Definition Classes

   Any

8. def clone(): AnyRef

   

   Attributes

   protected[java.lang]

   Definition Classes

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   Annotations

   @throws( ... )

9. def containsRefName(name: String): Boolean

   

   Checks to see if we have a contig with a given name.

   Checks to see if we have a contig with a given name.

   name

   The name of the contig to extract.

   returns

   True if we have a sequence record for this contig.

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

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    Annotations

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

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

    

    Definition Classes

    AnyRef → Any

14. val hasSequenceOrdering: Boolean

    

15. def hashCode(): Int

    

    Definition Classes

    SequenceDictionary → AnyRef → Any

16. def isCompatibleWith(that: SequenceDictionary): Boolean

    
    that

    Sequence dictionary to compare against.

    returns

    True if each record in this dictionary exists in the other dictionary.

17. def isEmpty: Boolean

    
    returns

    True if this dictionary contains no sequence records.

18. final def isInstanceOf[T0]: Boolean

    

    Definition Classes

    Any

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

    

    Definition Classes

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20. final def notify(): Unit

    

    Definition Classes

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21. final def notifyAll(): Unit

    

    Definition Classes

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22. val records: Vector[SequenceRecord]

    

    The individual reference contigs.

23. def size: Int

    

    The number of sequences in the dictionary.

24. 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

25. 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

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

    

    Definition Classes

    AnyRef

27. 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.

28. def toString(): String

    

    Definition Classes

    SequenceDictionary → AnyRef → Any

29. final def wait(): Unit

    

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    Annotations

    @throws( ... )

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

    

    Definition Classes

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    @throws( ... )

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

    

    Definition Classes

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    @throws( ... )