Loads and extracts sequences directly from indexed fasta or fa files.
Implements a traversable collection that is backed by a Parquet file.
A broadcastable ReferenceFile backed by a map containing contig name -> Seq[NucleotideContigFragment] pairs.
File that contains a reference assembly that can be broadcasted
Represents a set of reference sequences backed by a .
AttributeUtils is a utility object for parsing optional fields from a BAM file, or the attributes column from an ADAM file.
Object for reading Bedtools genome files from disk.
Helper object for setting the logging level for Parquet.
Helper singleton for converting Phred scores to/from probabilities.
Companion object for creating a ReferenceContigMap from an RDD of contig fragments.
Object for reading sequence dictionary files (.
Writes an RDD to disk as text and optionally merges.