SequenceDictionary

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. def contigLengths: ContigLengths

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

    Definition Classes

    AnyRef

14. def equals(o: Any): Boolean

    Definition Classes

    SequenceDictionary → AnyRef → Any

15. def finalize(): Unit

    Attributes

    protected[java.lang]

    Definition Classes

    AnyRef

    Annotations

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

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

    Definition Classes

    AnyRef → Any

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 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

26. 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

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

    Definition Classes

    AnyRef

28. 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.

29. def toString(): String

    Definition Classes

    SequenceDictionary → AnyRef → Any

30. final def wait(): Unit

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )

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

    Definition Classes

    AnyRef

    Annotations

    @throws( ... )