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.
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.