reference

Type Members

1. class ContigIterator[+T] extends BufferedIterator[T]

   Given some elements and a function for extracting a ContigName from them, return an iterator that is restricted to the given contig.

2. type ContigName = String

3. case class ContigNotFound(contigName: String, availableContigs: Iterable[String]) extends Exception with Product with Serializable

4. trait ContigSequence extends AnyRef

5. trait HasContig extends AnyRef

6. trait HasLocus extends AnyRef

7. trait Interval extends Ordered[Interval]

8. type Locus = Long

9. type NumLoci = Long

10. trait Position extends ReferenceRegion with HasLocus with PartiallyOrdered[Position]

11. case class ReferenceBroadcast(broadcastedContigs: Map[String, ContigSequence], source: Option[String]) extends ReferenceGenome with Product with Serializable

12. trait ReferenceGenome extends AnyRef

13. trait ReferenceRegion extends HasContig with Interval

    Trait for objects that are associated with an interval on the genome.