package util

  1. Public
  2. All

Type Members

  1. case class IndexedFastaFile(sc: SparkContext, filePath: String, stringency: ValidationStringency = ...) extends ReferenceFile with Logging with Product with Serializable

    Loads and extracts sequences directly from indexed fasta or fa files.

  2. class ParquetFileTraversable[T <: IndexedRecord] extends Traversable[T]

    Implements a traversable collection that is backed by a Parquet file.

  3. case class ReferenceContigMap(contigMap: Map[String, Seq[NucleotideContigFragment]]) extends ReferenceFile with Product with Serializable

    A broadcastable ReferenceFile backed by a map containing contig name -> Seq[NucleotideContigFragment] pairs.

  4. trait ReferenceFile extends Serializable

    File that contains a reference assembly that can be broadcasted

  5. class TwoBitFile extends ReferenceFile

    Represents a set of reference sequences backed by a .

  6. class TwoBitFileSerializer extends Serializer[TwoBitFile]

Value Members

  1. object AttributeUtils

    AttributeUtils is a utility object for parsing optional fields from a BAM file, or the attributes column from an ADAM file.

  2. object ParquetLogger

    Helper object for setting the logging level for Parquet.

  3. object PhredUtils extends Serializable

    Helper singleton for converting Phred scores to/from probabilities.

  4. object ReferenceContigMap extends Serializable

    Companion object for creating a ReferenceContigMap from an RDD of contig fragments.