util

Type Members

1. case class DeletionEvent(readName: String, eventOffset: Int, eventLength: Int, mapQ: Int, qual: Int) extends PileupEvent with Product with Serializable

2. case class InsertionEvent(readName: String, insertedSequence: String, mapQ: Int, qual: Int) extends PileupEvent with Product with Serializable

3. class IntervalListReader extends Traversable[(ReferenceRegion, String)]

   Reads GATK-style interval list files e.

4. case class MatchEvent(readName: String, isReverseStrand: Boolean, eventOffset: Int, eventLength: Int, mapQ: Int, qual: Int) extends PileupEvent with Product with Serializable

5. class MdTag extends AnyRef

   Represents the mismatches and deletions present in a read that has been aligned to a reference genome.

6. case class MismatchEvent(readName: String, mismatchedBase: Base.Value, isReverseStrand: Boolean, eventOffset: Int, eventLength: Int, mapQ: Int, qual: Int) extends PileupEvent with Product with Serializable

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

8. class Pileup extends Serializable

9. abstract class PileupEvent extends Serializable

10. class PileupTraversable extends Traversable[Pileup] with Serializable

11. class QualityScore extends Ordered[QualityScore] with Serializable

12. class RegExp extends AnyRef

    Wraps the java Pattern class, to allow for easier regular expression matching (including making the matches/finds methods return Option[Matcher], so that we can flatMap a set of strings with these methods).

13. class TwoBitFile extends AnyRef

    Represents a set of reference sequences backed by a .

14. case class TwoBitRecord(dnaSize: Int, nBlocks: Seq[ReferenceRegion], maskBlocks: Seq[ReferenceRegion], dnaOffset: Int) extends Product with Serializable