The individual reference sequences.
Adds a sequence record to this dictionary.
Adds a sequence record to this dictionary.
The sequence record to add.
A new sequence dictionary with the new record added.
Merges two sequence dictionaries.
Merges two sequence dictionaries.
Filters any sequence records that exist in both dictionaries.
The sequence dictionary to add.
A new sequence dictionary that contains a record per reference in each input dictionary.
The name of the reference to extract.
If available, the sequence record for this reference.
Checks to see if we have a reference with a given name.
Checks to see if we have a reference with a given name.
The name of the reference to extract.
True if we have a sequence record for this reference.
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.
Reference name to filter by.
SequenceDictionary filtered to include only those sequence records for the specified reference name
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.
Reference name filter function to filter by.
SequenceDictionary filtered 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 for the specified reference names.
Filter this sequence dictionary to include only those sequence records for the specified reference names.
Reference names to filter by.
SequenceDictionary filtered to include only those sequence records for the specified reference names
Sequence dictionary to compare against.
True if each record in this dictionary exists in the other dictionary.
True if this dictionary contains no sequence records.
The individual reference sequences.
The number of sequences in the dictionary.
Sort the records in a sequence dictionary.
Sort the records in a sequence dictionary.
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.
stripIndices
Strips indices from a Sequence Dictionary.
Strips indices from a Sequence Dictionary.
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.
sorted
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 a SAM formatted sequence dictionary.
A SequenceDictionary contains metadata about the reference build genomic data is aligned against.
SequenceRecord