The individual reference contigs.
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 contig in each input dictionary.
The name of the contig to extract.
If available, the sequence record for this contig.
Checks to see if we have a contig with a given name.
Checks to see if we have a contig with a given name.
The name of the contig to extract.
True if we have a sequence record for this contig.
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 contigs.
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 contig 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