org.bdgenomics.adam.models

# SequenceDictionary

#### class SequenceDictionary extends Serializable

A SequenceDictionary contains metadata about the reference build genomic data is aligned against.

See also

  SequenceRecord

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### Instance Constructors

1. #### new SequenceDictionary()

2. #### new SequenceDictionary(records: Vector[SequenceRecord])

   records

     The individual reference contigs.

### 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. #### 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.

5. #### 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.

6. #### final def ==(arg0: AnyRef): Boolean

   Definition Classes
     AnyRef

7. #### final def ==(arg0: Any): Boolean

   Definition Classes
     Any

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

   name

     The name of the contig to extract.

   returns

     If available, the sequence record for this contig.

9. #### final def asInstanceOf[T0]: T0

   Definition Classes
     Any

10. #### def clone(): AnyRef

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

11. #### 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.

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

    Definition Classes
      AnyRef

13. #### def equals(o: Any): Boolean

    Definition Classes
      SequenceDictionary → AnyRef → Any

14. #### def finalize(): Unit

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

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

    Definition Classes
      AnyRef → Any

16. #### val hasSequenceOrdering: Boolean

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

    Definition Classes
      SequenceDictionary → AnyRef → Any

18. #### def isCompatibleWith(that: SequenceDictionary): Boolean

    that

      Sequence dictionary to compare against.

    returns

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

19. #### def isEmpty: Boolean

    returns

      True if this dictionary contains no sequence records.

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

    Definition Classes
      Any

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

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

    Definition Classes
      AnyRef

24. #### val records: Vector[SequenceRecord]

    The individual reference contigs.

25. #### def size: Int

    The number of sequences in the dictionary.

26. #### 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

27. #### 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

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

    Definition Classes
      AnyRef

29. #### 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.

30. #### def toString(): String

    Definition Classes
      SequenceDictionary → AnyRef → Any

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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

    Definition Classes
      AnyRef
    Annotations
      @throws( ... )

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