class SequenceDictionary extends Serializable

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

See also

SequenceRecord

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  1. SequenceDictionary
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Instance Constructors

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

    records

    The individual reference sequences.

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 reference 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 reference to extract.

    returns

    If available, the sequence record for this reference.

  7. final def asInstanceOf[T0]: T0
    Definition Classes
    Any
  8. def clone(): AnyRef
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native() @HotSpotIntrinsicCandidate()
  9. def containsReferenceName(name: String): Boolean

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

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

    name

    The name of the reference to extract.

    returns

    True if we have a sequence record for this reference.

  10. final def eq(arg0: AnyRef): Boolean
    Definition Classes
    AnyRef
  11. def equals(o: Any): Boolean
    Definition Classes
    SequenceDictionary → AnyRef → Any
  12. def filterToReferenceName(referenceName: String): SequenceDictionary

    Filter this sequence dictionary to include only those sequence records for the specified reference name.

    Filter this sequence dictionary to include only those sequence records for the specified reference name.

    referenceName

    Reference name to filter by.

    returns

    SequenceDictionary filtered to include only those sequence records for the specified reference name

  13. def filterToReferenceNames(fn: (String) ⇒ Boolean): SequenceDictionary

    Filter this sequence dictionary to include only those sequence records with reference names that pass the specified filter function.

    Filter this sequence dictionary to include only those sequence records with reference names that pass the specified filter function.

    fn

    Reference name filter function to filter by.

    returns

    SequenceDictionary filtered to include only those sequence records with reference names that pass the specified filter function

  14. def filterToReferenceNames(referenceNames: Iterable[String]): SequenceDictionary

    Filter this sequence dictionary to include only those sequence records for the specified reference names.

    Filter this sequence dictionary to include only those sequence records for the specified reference names.

    referenceNames

    Reference names to filter by.

    returns

    SequenceDictionary filtered to include only those sequence records for the specified reference names

  15. final def getClass(): Class[_]
    Definition Classes
    AnyRef → Any
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  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
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  23. final def notifyAll(): Unit
    Definition Classes
    AnyRef
    Annotations
    @native() @HotSpotIntrinsicCandidate()
  24. val records: Vector[SequenceRecord]
  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 reference 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(arg0: Long, arg1: Int): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )
  32. final def wait(arg0: Long): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... ) @native()
  33. final def wait(): Unit
    Definition Classes
    AnyRef
    Annotations
    @throws( ... )

Deprecated Value Members

  1. def finalize(): Unit
    Attributes
    protected[lang]
    Definition Classes
    AnyRef
    Annotations
    @throws( classOf[java.lang.Throwable] ) @Deprecated @deprecated
    Deprecated

    (Since version ) see corresponding Javadoc for more information.

Inherited from Serializable

Inherited from Serializable

Inherited from AnyRef

Inherited from Any

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