org.bdgenomics.adam.rdd.contig
From a set of contigs, returns the base sequence that corresponds to a region of the reference.
From a set of contigs, returns the base sequence that corresponds to a region of the reference.
Reference region over which to get sequence.
String of bases corresponding to reference sequence.
Throws exception if query region is not found.
Aggregates together a sequence dictionary from the different individual reference sequences used in this dataset.
Aggregates together a sequence dictionary from the different individual reference sequences used in this dataset.
A sequence dictionary describing the reference contigs in this dataset.
Counts the k-mers contained in a FASTA contig.
Counts the k-mers contained in a FASTA contig.
The length of k-mers to count.
An optional sequence dictionary. If none is provided, we recompute the sequence dictionary on the fly. Default is None.
Returns an RDD containing k-mer/count pairs.
For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.
For all adjacent records in the RDD, we extend the records so that the adjacent records now overlap by _n_ bases, where _n_ is the flank length.
The length to extend adjacent records by.
An optional sequence dictionary. If none is provided, we recompute the sequence dictionary on the fly. Default is None.
Returns the RDD, with all adjacent fragments extended with flanking sequence.
For a single RDD element, returns 0+ sequence record elements.
For a single RDD element, returns 0+ sequence record elements.
Element from which to extract sequence records.
A seq of sequence records.
Merge fragments by contig name.
Save nucleotide contig fragments in FASTA format.
Save nucleotide contig fragments in FASTA format.
file name
hard wrap FASTA formatted sequence at line width, default 60
Converts an RDD of nucleotide contig fragments into reads.
Converts an RDD of nucleotide contig fragments into reads. Adjacent contig fragments are combined.
Returns an RDD of reads.