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. implicit final class ContigLengths extends AnyVal

3. case class ContigName extends Ordered[ContigName] with Product with Serializable

4. trait ContigSequence extends BasesBuffer

5. class ContigsIterator[T] extends SimpleBufferedIterator[(ContigName, ContigIterator[T])]

   Divide an iterator into a series of contig-restricted iterators.

6. trait HasContig extends Any

7. trait HasLocus extends Any

8. trait Interval extends Any

9. type KmerLength = Int

10. case class Locus(locus: LociT) extends Ordered[Locus] with Comparable[Locus] with Product with Serializable

11. type NumLoci = Locus

12. case class Position(contigName: ContigName, locus: Locus) extends Region with HasLocus with Product with Serializable

    Base trait for classes that logically exist at one genomic locus.

13. trait Region extends HasContig with Interval

    Trait for objects that are associated with an interval on a genomic contig.

14. class Registrar extends KryoRegistrator

15. case class RepeatedContigException(msg: String) extends Exception with Product with Serializable

16. case class Slice(contigName: ContigName, start: Locus, bases: Bases) extends Region with Product with Serializable

17. implicit final class WindowSize extends AnyVal with Ordered[Int]