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
- new SequenceDictionary()
-
new
SequenceDictionary(records: Vector[SequenceRecord])
- records
The individual reference sequences.
Value Members
-
final
def
!=(arg0: Any): Boolean
- Definition Classes
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final
def
##(): Int
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-
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.
-
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.
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final
def
==(arg0: Any): Boolean
- Definition Classes
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-
def
apply(name: String): Option[SequenceRecord]
- name
The name of the reference to extract.
- returns
If available, the sequence record for this reference.
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final
def
asInstanceOf[T0]: T0
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def
clone(): AnyRef
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- protected[lang]
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- @throws( ... ) @native() @HotSpotIntrinsicCandidate()
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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.
-
final
def
eq(arg0: AnyRef): Boolean
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def
equals(o: Any): Boolean
- Definition Classes
- SequenceDictionary → AnyRef → Any
-
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
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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
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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
-
final
def
getClass(): Class[_]
- Definition Classes
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- @native() @HotSpotIntrinsicCandidate()
- val hasSequenceOrdering: Boolean
-
def
hashCode(): Int
- Definition Classes
- SequenceDictionary → AnyRef → Any
-
def
isCompatibleWith(that: SequenceDictionary): Boolean
- that
Sequence dictionary to compare against.
- returns
True if each record in this dictionary exists in the other dictionary.
-
def
isEmpty: Boolean
- returns
True if this dictionary contains no sequence records.
-
final
def
isInstanceOf[T0]: Boolean
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final
def
ne(arg0: AnyRef): Boolean
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final
def
notify(): Unit
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final
def
notifyAll(): Unit
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- val records: Vector[SequenceRecord]
-
def
size: Int
The number of sequences in the dictionary.
-
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
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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
-
final
def
synchronized[T0](arg0: ⇒ T0): T0
- Definition Classes
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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.
-
def
toString(): String
- Definition Classes
- SequenceDictionary → AnyRef → Any
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final
def
wait(arg0: Long, arg1: Int): Unit
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final
def
wait(arg0: Long): Unit
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final
def
wait(): Unit
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def
finalize(): Unit
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